Gromacs - Science topic

I was performing free energy calculation using g_mmpbsa tools. From the summary data i got the value of binding energy, but when i check the output file, it shows only data energy for the complex. Meanwhile we need to calculate the energy component of protein, ligand, and protein-ligand complex to get the binding free energy. so is that means that we have to perform the calculation for protein, ligand, and complex separately?

Thank you

When i run the command to calculate the H-bonds ''gmx hbond -s md.tpr -f md_center.xtc -num hb.xvg'' I can't find anything ( the file hb.xvg does not contain the number of H-bonds).

I also tchecked the complex.gro and i analyzed the RMSD, RMSF, Rg successfully.

I use Gromacs 2023.

I’m using force field parameters from a paper, building the top file in gromacs. I’m a bit stuck on the concept of multiplicity for improper dihedrals.

My questions are:

Thanks, Yehonatan

Dear ResearchGate community,

I have recently conducted two separate 100 ns molecular dynamics simulations using GROMACS, each involving a small molecule. My analysis of hydrogen bonding patterns has revealed an unexpected observation: zero hydrogen bonding and an unusually large number of pairs within 0.35 nm. For instance, at a specific time point (e.g., time = 1.90108e-33 ns), the number of hydrogen bonds reported is >1110000000. I would like to know about such variations and how should I fix it, and if anyone has insights into the potential implications of this observation. I appreciate any feedback or experiences you can share on this matter.

; Include forcefield parameters

#include "./charmm36-mar2019.ff/forcefield.itp"

; Include ligand parameters

#include "crx.prm"

Thank you

Can anyone help me parametrize Si atoms in gromacs forcefields. how can i include parameters in ffnonbonded and bonded and atomtype files of gromacs forcefield for example oplsaa or charmm? (I want to perform md simulation of silica nanoparticles with gromacs and i dont know how)

Hello everyone I’m trying to run a MD simulation in acetonitrile as solvent but when I execute gmx-solvate command, solvent molecules break apart making the number of atoms in .gro and .top files different from one another. Does anyone know how this issue can be addressed? I appreciate any help in advance.

I am running the MD simulations for 50000000 steps using GROMACS software but it has terminated (after 36000000 steps) before completion due to power off. I would like to continue the same calculation to complete the simulation.

I am currently going through the following tutorial for replica exchange MD on gromacs: https://www.gromacs.org/@api/deki/files/209/=tutorial.pdf

When I got to stage 2 and tried to create the .tpr files using the command,

(for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t equil-state; cd ..; done)

I get this error:

Program: gmx grompp, version 2018.2

Source file: src/gromacs/fileio/checkpoint.cpp (line 531)

Function: int doVectorLow(XDR*, StatePart, int, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator<int>; XDR = XDR; FILE = _IO_FILE]

Assertion failed:

Condition: list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr)

Without list, we should have exactly one of v and vector != NULL

I have no idea why this error is occurring, as I'm following the tutorial almost exactly. From searching online, it seems like other people have came across a similar problem, although I can't find any solutions.

Any help would be appreciated!

Hello every body

I want to do umbrella sampling following Mr. Justin Lemkul Tutorial. I simulated and prepared lipid bilayer by version 4 of gromacs before, now in continuous in order to do the umbrella sampling tutorial (which is updated to version 5.x. ) I want to know whether I have to simulate the lipid bilayer again with v. 5.x of gromacs to continue umbrella sampling or its not nessasery.

thanks.

Hi, I am doing simulation of 2 proteins, one is a protein fibril having 5 chains and another is the unfolded monomer, there are total 740 residues. After nvt equillibration the protein is going out of the water box. I have taken a truclinic box, having 3.3 lakh atoms. How to solve the issue? I am attaching the image of the .gro file got from nvt.

Hello researchers,

I have processed a MD simulation study of 26 amino acid amylose chain in water using gromacs. Now i want to analyze Dihedral angle for the glucose residues alpha 1-4 linkage, defined by atoms O5-C1-O4'-C4' (phi) and C1-O4'-C4'-C3' (psi).

I tried generating angular index file for dihedral angles, showing various phi angles. I also tried also check various publication but none of them have mentioned the methodology to calculate dihedral angles.

Please help me with the calculation of dihedral angles.

Thank you in anticipation.

Dear All, I want to make a side-chain stapling of lysine (or its non-standard amino acid derivatives). How to make a topology file for this kind of side-chain stapling (I believe, it is not possible via CHARMM-GUI Solution Builder), without using CGENFF? Please suggest ways for this. PS. The stapling method is shown in the attached image. Thank You

Respected Researchers,

I have six i7 computers with 4 physical cores and each core with 2 threads and all are connected with LAN. Therefore, I want to run the GROMACS in parallel (cluster).

I have successfully mounted them using ssh, nfs and OpenMPI.

Afterwards I successfully installed GROMACS using below command.

cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_BUILD_TYPE=Release -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_BUILD_UNITTESTS=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_BUILD_MDRUN_ONLY=ON

Then I used "mpirun -np 12 gmx_mpi mdrun -ntomp 2 -npme 2" but it run on single computer only.

I think I am doing something wrong. Please help, I am very new in computers and commands.

Thank you

I have a system of DNA and a certain molecule that shows good docking energy with DNA. I want to run the simulation in gromacs. The parameters I should use for DNA is amberff99parmbsc so I tried getting parameters for the molecule as per the tutorial using parmcheck and acpype. Unfortunately one of the elements of my molecule is non-standard element so the tutorial doesn't seem to work. My question is do we have some other way to get the forcefield parameters for the new molecule? My second question is can I use CHARMM parameters for my molecule and AMBER for DNA?

Dynamic Non-equilibrium Molecular Dynamics

For example, I have quercetine as a ligand and cutinase as protein. If i want to carried out md simulations with different concentration of quercetine, how to do that? I want to do md simulations by 50ng/ul of quercetine. Please help me. I'm using gromacs for simulations

Hi,

I'm new at MD. so I want to know more about protein preparation steps.

I wanna work with gromos54a3

and

is it important to edit orientation of these residues CYS, GLN, ASN? WHY?

and

is it important to edit protonation state of these residues CYS, LYS, GLN, ASP, HIS? WHY?

Dear All,

I am trying to simulate a dimer and would like to restrain a part of it on both chains. not a problem and the error is commonşy reported. so i tried all teh suggestions but none is working as grompp is accepting one of the posres files but throws the error for the other one. my toplogy file looks like this.

---------------

; Include chain topologies

#include "topol_Protein_chain_A.itp"

;; Include CRD Position restraint file for Chain A

#ifdef POSRES_CRD_A

#include "posre_crd_chain_A.itp"

#endif

#include "topol_Protein_chain_B.itp"

; Include CRD Position restraint file for Chain B

#ifdef POSRES_CRD_B

#include "posre_crd_chain_B.itp"

#endif

#include "topol_Ion_chain_A2.itp"

#include "topol_Ion_chain_B2.itp"

#include "topol_Protein_chain_A3.itp"

#include "topol_Protein_chain_B3.itp"

; Include water topology

#include "./charmm36-jul2022.ff/spce.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include topology for ions

#include "./charmm36-jul2022.ff/ions.itp"

[ system ]

; Name

2 Protein in water

[ molecules ]

; Compound #mols

Protein_chain_A 1

Protein_chain_B 1

Ion_chain_A2 1

Ion_chain_B2 1

Protein_chain_A3 1

Protein_chain_B3 1

SOL 111424

NA 48

--------------------

any suggestions are appreciated.

thank you

ayesha

I am adding the Graph result below. The whole trajectory run was 20 ns. is there any particular threshold value for H-bond?

Good day all, i encountered a strange problem with gromacs when restarting my simulation. i ran a 100ns simulation and then created a new tpr file named newproduction.tpr to extend my simulation using convert-tpr. since i initially did not want to append i used the command gmx_mpi mdrun -deffnm newproduction -cpi state.cpt -noappend to create a new xtc, log, trr, edr, and cpt files but when i want to append to my new xtc files i get an input/output error. the problem is that gromacs is recognizing my log file as newproduction.part0008.part008.log but in my directory the name is newproduction.part0008.log i don't understand why gromacs is recognizing my new xtc files but not my log file

Actually,as far as I know to see the strength of protein-ligand interaction for drug discovery pupose it is very important parameter need to be calculated. Due to update in the gromacs version this is getting difficult.Kindly help me with this if there is any other alternative to this too.

I want to perform a molecular dynamic simulation of a covalent organic framework(COF) in Gromacs using the CHARMM36 force field. The COF has 384 atoms and I have a problem with parametrizing and getting the right topology because CGenFF and Swissparam both can't calculate the parameters of COF due to the hundreds of atoms.

Are there alternative websites or any other ways to get parameters?

I have done 10ns Simulation of complex(Protein ligand) by gromacs tutorial command but for further extend for 200ns. I did by tutorial and confusion please guide?

Thankyou in Advance.

Dear All

Can any one suggest command for density distribution and secondary structure calculation of protein-ligand complex in gromacs.

Hello,

I want to use the final structure of gromacs after 100ns to run a GaMD simulation with amber software. So，I should turn the gromacs' top and gro files into amber's parm and rst files?

I searched on the Internet that parmed can be transferred, but our server's parmed software cannot be used.

Is there any other way to turn them?

Thank.

I am trying to perform simulation of my protein-ligand complex system following Gromacs Protein-Ligand complex tutorial , so during the NVT equilibration using the command

" gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr"

iI encountered an error

i am using gmx version 2022

enclosing nvt.mdp input file

how to solve this error ?

Dear all,

I have been trying to create a complex for MD simulation in gromacs of Calcium sensing receptor venus fly trap domain with tryptophan in the binding site as it is part of the crystal structure. However, there is an OXT terminal oxygen which CHARMM 36 does not read and a nitrogen atom N that OPLS-AA gives an error for.

I am stumped. I tried using the CHARMM-GUI to create the ligand files for gromacs but it also has an OXT oxygen atom. I used the bound ligand as well as a fresh ligand from pubchem, the problem remains that it is not recognised by Charmm ff.

Please let me know how to prepare my complex?

/usr/include/c++/11/type_traits:3071:7: note: ‘std::__is_complete_or_unbounded<std::__type_identity<gmx::IndexGroupsAndNames> >((std::__type_identity<gmx::IndexGroupsAndNames>{}, std::__type_identity<gmx::IndexGroupsAndNames>()))’ evaluates to false

make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:21782: src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o] Error 1

make[1]: *** [CMakeFiles/Makefile2:4537: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2

make: *** [Makefile:166: all] Error 2

bash: line 9: /usr/local/gromacs/bin/GMXRC: No such file or directory

---------------------------------------------------------------------------

Can someone help me? The authors have extracted the conformations of different free energy states and compared the motions....I know it's a Free energy landscape and how to generate it through sham module of gromacs...but how to extract a conformation of particular energy state and how to know their timeframe in the trajectory?

Hello!

The protein of my interest has a covalently bound inhibitor, which is a sulfone compound. I am currently trying to prepare all the files necessary for the MD simulation and use CGenFF server to generate topology of the modified residue (with the inhibitor bound). However, CGenFF is unable to recognize the sulfur type and generates the following error: "attype warning: unknown sulfur type not supported;skipped molecule".

Is there any way to fix this problem or do I have to choose another way of creating the topology file? Can you give me any recommendations on which servers I can use instead then?

Any advice would be appreciated.

2 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.

I got this error while performing gmx mdrun -deffnm nvt

Any solution for this?

I am using the NEMD method to calculate the thermal conductivity of water in Gromacs. I have three groups in the simulation: hot water, cold water, and free water. I want to calculate the kinetic energy of each group.

Here is the method I used:

1. Using gmx select to isolate the group, producing an index file.

2. With the convert-tpr command, I can create a modified .tpr file centered on the selected group.

3. The gmx trjconv command extracts the group's coordinates from the entire trajectory to obtain a group-specific trajectory.

4. With the modified .tpr file and the group-specific trajectory, the gmx mdrun command with the -rerun option recalculates the energies for the specific group, generating a new energy file. This energy data can then be extracted and analyzed using gmx energy.

However, there is no option for the kinetic energy. What I got is attached. Any suggestions would be very appreciated!

I am writing to seek assistance on a matter related to n2t file generation. I am using GROMACS and charmm36 force field in my work. I am covalently attaching a short polymer(poly-peptide) to a nanosheet with the carbonyl carbon of the polymer attached to the nitrogen of the nanosheet I obtained the parameter(itp file) for the polypeptide from CGENFF then added the corresponding atom types and charges from the itp to my n2t file the monomer of the poly-peptide is histidine and it’s itp file has various hydrogen atom type along with carbon types with different charges I have added them all in the n2t file in the same sequence as in the itp since most these atom types are attached to carbon when topology is created using x2top wrong type of carbon and consequently wrong charge is assigned to the atom of my structure. I want you to note the hydrogen types as well as the nitrogen type NG2R51 in the topology file at line 134 it is supposed to be a NG2S1 nitrogen type with a -0.555 charge. There are many other atoms whose atom type was supposed to be different. How can I obtain correct topology.I am attaching the itp file(plh.itp) along with the ss of topology and n2t file. Any guidance or pointers would be of immense help. Thank you for your time.

Hi every body. I want to do a MD in gromacs for protein but it have a non standard residue. Somone who tell me how I can to do it? Which programs I should to usage? or some tutorial that I can to do or see for this. The protein is GABA AMINOTRANSFERASE but this contain whit PLP covalent bond to LYS residue. THANKS

I selected Md_0_10.gro file and then md_0_10.xtc file then I got something weird like this in the video in vmd, can someone pls suggest what's wrong in this step?

I have faced a problem in PCA analysis. I had done PCA analysis of 5 protein-ligand complex in GROMACS. The reviewer asked me to add eigenvectors and eigenvalues plot. I added a plot of eigenvalues vs eigenvector indices. But again he asked me same question “Add to your result and to your figure 6 plots the eigenvectors and eigenvalues. How the eigenvectors explain the variability in the plots?”

Hi Everyone,

GROMACS version:2022.1((single precision) GROMACS modification: Yes/No Hi Everyone, Today I am running my second protein ligand simulation(read I am new to GROMACS) I am using a LINUX server cluster of following configurations: $ lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 24 On-line CPU(s) list: 0-23 Thread(s) per core: 1 Core(s) per socket: 12 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 63 Model name: Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz Stepping: 2 CPU MHz: 1200.042 BogoMIPS: 4594.33 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 30720K NUMA node0 CPU(s): 0-11 NUMA node1 CPU(s): 12-23 I am running a protein-ligand simulation of 500ns having the following atoms : Compound #atoms Protein 140 residues ligand 71 SOL 317409 H2O molecules SOD 9 I used md.mdp file as follows: title = Protein-ligand complex MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 250000000 ; 2 * 5000000 = 10000 ps (500 ns) dt = 0.002 ; 2 fs ; Output control nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save coordinates every 10.0 ps ; Bond parameters continuation = yes ; continuing from NPT constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighbor searching and vdW cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 20 ; largely irrelevant with Verlet rlist = 1.2 vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.2 pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_ligan SOL_SOD ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction is not used for proteins with the C36 additive FF DispCorr = no ; Velocity generation gen_vel = no ; continuing from NPT equilibration

I used the command nohup mpiexec -np 24 gmx_mpi mdrun -deffnm md -v, and unbearably, it shows that it will finish Thu Jun 13 04:47:54 2024. Please suggest anything to fasten up the process. I would be grateful for suggestions/help Thanks in advance

Dear all, I am attempting to download PLUMED in order to conduct enhanced sampling using Gromacs 3 2020. Could you please inform me which version of PLUMED would be compatible with Gromacs 3 2020? Kind regards.

I am going to do md simulation of 10 receptor-ligand complex. Is the gmx_energy function is enough to decide the binding strength or I have to do gmx_mmpbsa to find free binding energy ? Is interaction energy or binding free energy are different and what they convey, is they are positively correlated?

I want to calculate the "secondary structure" of protein after the MD simulation so i wanted to install "dssp "in gromacs i tried but i can't able to install i was getting error so please can anyone tech me how to install and use for it.

Thank You !!

Hi everyone,

Do you have any idea how we can use

NPH ensemble in Gromacs?

Do we need to completely delete temperature coupling options and use Parrinello-Rahman as the barostat(or maybe c-rescale)?

Should any extra settings be considered?

Best

hi

I wanted to draw diagram" the relative shape asymmetry parameter for inclusion of ligand into the b-CD cavity" with gromacs.

I kindly beseech your counsel and guidance in navigating this endeavor.

Dear all

I have few confusions about the pulling code in gromacs, I was using NAMD before and the method was quite straighforward in NAMD to pull the ligand out of the protein, in gromacs it is also straight forward but I need to clear few things

1. In NAMD one can define the pulling direction by using SMDDir in the input file. Difference between the COM distance of SMD atom and fixed atom gives the pulling direction, SMD atoms are usually the heavy atoms of the ligand whereas the CA backbone of the protein is kept fixed. This difference between the COM distances of both tells the pulling direction of the ligand in NAMD in case one does not know the pulling direction of the ligand. Is pull-coord1-vec is same as NAMD SMDDir ? And in NAMD you define the SMD atoms and fixed atoms, here in Gromacs I am confused how it defines the fixed atoms or reference atom which is protein from where ligand has to be pulled out?

I followed the umbrella sampling tutorial in Gromacs

2. Secondly I did few tests regrading pulling out the ligand from the protein using the pull code as below, this is just a test code to understand things thats why applied quite fast velocity.

; Pull code

pull = yes

pull_ncoords = 1 ; only one reaction coordinate

pull_ngroups = 2 ; two groups defining one reaction coordinate

pull_group1_name = Ligand

pull_group2_name = Protein

pull_coord1_type = umbrella ; harmonic potential

pull_coord1_geometry = distance ;

pull-coord1-vec = -0.49 -0.85 0.16 ;

; pull-coord1-origin = 53.12 52.96 53.066

pull_coord1_dim = Y Y Y ;

pull_coord1_groups = 1 2 ;

pull-pbc-ref-prev-step-com = YES

pull-group1-pbcatom = 0

;pull-group2-pbcatom = 0

pull_coord1_start = yes ; define initial COM distance > 0

pull_coord1_rate = 0.01 ; 0.0004 nm per ps

pull_coord1_k = 600 ; kJ mol^-1 nm^-2

I changed one parameter of the pulling code every time to see whether there is any affect on the pulling but by visualizing the trajectories I didn't see any difference, the ligand is still coming out even if I switch off pull-coord1-vec, pull_coord1_dim together. Also with these feature if I changed distance to direction still the ligand comes out.

Secondly if I just keep pull_coord1_dim Y Y Y in all three dimensions it still takes the ligand out of the protein in almost similair direction as given by pull-coord1-vec, if I dont give pull-coord1 vec and only give pull coord1 dim Y Y Y will my ligand be pulled in a random direction?

Also What is pull-coord1-origin? is it the origin of the box?

Anyone kindly let me know what changes should I make in the above given code where I just want my ligand to come out of the protein in a random pulling direction or by the method of NAMD SMDDir?

I am mostly interested in the pulling forces required to pull the ligand, so what should be the pulling code input in gromacs for that?

Thank you in advance, your answer will help me in understanding the pulling code and applying it to my work!!

While trying to run the MD simulation with the CHARMM-GUI input file, I encounter such an error during the equilibration phase. How to overcome this?

gmx mdrun -v -deffnm ${istep}

Program: gmx mdrun, version 2023-Homebrew

Source file: src/gromacs/mdlib/sim_util.cpp (line 554)

Function: void checkPotentialEnergyValidity(int64_t, const gmx_enerdata_t&, const t_inputrec&)

Internal error (bug):

Step 0: The total potential energy is 1.03605e+19, which is extremely high.

The LJ and electrostatic contributions to the energy are 1.03605e+19 and

-2.96596e+06, respectively. A very high potential energy can be caused by

overlapping interactions in bonded interactions or very large coordinate

values. Usually this is caused by a badly- or non-equilibrated initial

configuration, incorrect interactions or parameters in the topology.

GROMACS version: GROMACS modification: Yes/No Here post your question I use the gromacs with the oficial docker image (https://hub.docker.com/r/gromacs/gromacs) and the mdrun of the main simulation returns this: /gromacs/bin/gmx: line 17: 1345054 Segmentation fault (core dumped) /gromacs/bin. ARCH/gmxmpi @ I would like to know if it is any mistake of mine and how to fix this. Att. Vicente Pires.

Best regard,

I get an error when I try to compile the * .sln file in VS 2019, after being generated by the Cmake interface.

My error output is:

"Compile operation started: project: release-version-info, configuration: Debug x64 ------

1> Generating release version information

1> - The source code for this GROMACS installation is different from the officially released version.

2> ------ Compile operation started: project: libgromacs, configuration: Debug x64 ------

2> Building NVCC (Device) object src / gromacs / CMakeFiles / libgromacs.dir / nbnxm / cuda / Debug / libgromacs_generated_nbnxm_cuda.cu.obj

2> nvcc fatal: Unknown option '-std: c ++ 17'

2> CMake Error at libgromacs_generated_nbnxm_cuda.cu.obj.Debug.cmake: 224 (message):

2> Error generating

2> C: /Users/USUARIO/Downloads/gromacs-2021.2/build/src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/cuda/Debug/libgromacs_generated_nbnxm_cuda.cu.obj

2>

2>

2> C: \ Program Files (x86) \ Microsoft Visual Studio \ 2019 \ Community \ MSBuild \ Microsoft \ VC \ v160 \ Microsoft.CppCommon.targets (241.5): error MSB8066: Custom build of "C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda_data_mgmt.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda_kernel_F_noprune.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda_kernel_F: USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda_kernel_VF_noprune.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda_prune_cu; C: USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ cuda \ nbnxm_cuda_kernel_pruneonly.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ domdec \ gpuhaloexchange_impl.cu; C: \ Users \ USUARIO Downloads \ gromacs-2021.2 \ src \ gromacs \ utility \ cuda_version_information.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ mdlib \ leapfrog_gpu.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ mdlib \ lincs_gpu.cu; C: \ Users \ USUARIO \ Downloads \ gromacs-2021.2 \ src \ gromacs \ mdlib \ settle_gpu.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ mdlib \ update_constrain_gpu_impl.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ mdlib \ gpuforcereduction_impl.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ listed_forces \ gpubonded_impl.cu; C: \ Users \ USUARIO \ Downloads \ gromacs-2021.2 \ src \ gromacs \ listed_forces \ gpubondedkernels.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ nbnxm \ nbnxm_gpu_data_mgmt.cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_ .cu; C: \ Users \ USUARIO \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_gpu_3dfft.cu; C: \ Users \ USUARIO \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_solve.cu; C : \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_spread.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_gpu_program_impl.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_pp_comm_gpu_impl.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pmeg_force_force_sender. cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_coordinate_receiver_gpu_impl.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_gpu_internal.cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ ewald \ pme_gpu_timings.cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ gpu_utils \ device_stream_manager.cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ gpu_utils \ device_stream.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ gpu_utils \ gpu_utils.cu; C: \ Users \ USER \ Downloads \ gromacs -2021.2 \ src \ gromacs \ gpu_utils \ pinning.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ gpu_utils \ pmalloc_cuda.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ hardware \ detecthardware.cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ h ardware \ device_management_common.cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ hardware \ device_management.cu; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ src \ gromacs \ mdtypes \ state_propagator_data_gpu_impl. cpp; C: \ Users \ USER \ Downloads \ gromacs-2021.2 \ build \ CMakeFiles \ a9116bcf4bc4115e626ce4c6578cc5c1 \ baseversion-gen.cpp.rule "terminated with code 1.

2> Compilation of project "libgromacs.vcxproj" finished - ERROR.

3> ------ Compile operation started: project: gmx, configuration: Debug x64 ------

3> LINK: fatal error LNK1104: cannot open file '.. \ .. \ lib \ Debug \ gromacs.lib'

3> Compilation of project "gmx.vcxproj" finished - ERROR.

========== Compile: 1 correct, 2 incorrect, 15 updated, 0 skipped ========== ".

I have CUDA 11.4, Win 10 64bit and FFTW 3.3.5 installed. I would be very grateful if you could guide me in solving this error, as I wish to be able to compile on my own any new version of Gromacs on Windows that might be released in the future.

Hello All

During the gromacs 2023.1 multiple ligand simulation , I have some problems and constraints in the simulation. In the experiments, I used AMBER99sb forcefield.

How to perform multiple ligand simulations

Whether i have to make different topology files for different ligands? because when trying to simulate at the ionization stage to get the ions.tpr file an error occurs as below:

Command line:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry 'title'

Ignoring obsolete mdp entry 'ns_type'

NOTE 1 [file ions.mdp]:

With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

that with the Verlet scheme, nstlist has no effect on the accuracy of

your simulation.

Setting the LD random seed to 2095054833

Generated 3486 of the 3486 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 3486 of the 3486 1-4 parameter combinations

-------------------------------------------------------

Program: gmx grompp, version 2023.1

Source file: src/gromacs/gmxpreprocess/topio.cpp (line 577)

Fatal error:

Syntax error - File entacapone1_GMX.itp, line 3

Last line read:

'[ atomtypes ]'

Invalid order for directive atomtypes

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

please help me to solve this problem, and I will be very grateful to you

Thankyou All

I want to perform MD Simulation of Ionic compounds in Gromacs but facing problems at various points.

One of my approaches of the work is submitting the pdb files of the cations and anions to ATB server to obtain the .itp files and Gromos 54a7.ff. I build the topology from these files.

I use packmol to pack 500 anions and cations pdb files in one box and then change them to .gro.

When I proceed to minimization with this .gro file and topolgy file, Gromacs prompt fatal error of mismatch of all the atoms in topology and .gro file.

I use charmm-gui to model the cation and anion with charmm forcefield in the topology but face the same problem.

Cgenff method as in protein-ligand complex simulation gave me broken cation_ini.pdb (since the number of atoms is correct I neglect this ) but when I proceed to combine the .gro files of the ions, like proten-ligand complex to get one structure file, they appear covalently bonded or scattered in the space which is not the correct chemistry of ionic compounds.

Ligpargen, Polypargen, Acpype, and TppMkTOP servers returns error whenever I submit either of the ions to get the topology file from them.

When I use AmberTools23, I got error at the step of packing the ions together and saving the prmtop and rst7/inpcrd files of the system.

I do appreciate your patience and guiding replies.

I know that gromacs uses cuda cores of Nvidia GPUs to run. But Nvidia GPUs are excessively priced and not future proof at all. But on the other hand inelt arc GPUs (let's conside the a770) offer the best bang for buck right now in the market. So is this possible to run mds in Intel gpu?

Did anyone have any success with it?

#gromacs #gpu #moleculardynamics #mds #dynamicsimulation

Dear research gate community,

I am trying to simulate a boron nitride nanosheet covalently functionalized with a short chain polymer using charmm36 force field in gromacs. I obtained the str file of polymer from cgenff and obtained its prm and itp file. Later I prepared a n2t file for the system including the nanosheet atoms and polymer atoms( the atom types were defined as per the atom types in itp file ).I was able to generate the topology file but I am doubtful about my approach as I only used atom types and charges and not the whole itp all the parameter like bond angles, dihedrals were automatically generated. It would be great if someone could guide me whether the approach is correct or not and how can i incoporate the itp parameter for the polymer. Any guidance would be of great value. Thank you!

#charmm36 #GROMACS #CGENFF

gmx_mmpbsa, error,

Does the python script, i.e. cgenff_charmm2gmx_py3_nx2.py (for CHARMM36) also works for a different force field such as CHARMM27 or AMBER99 SB or GROMOS96 54A7 ?

if not, where can I find the script for (each respective force field) generating ligand topology files such as .prm, .pdb and .itp ?

Is there any other way you may suggest to generate ligand topology files such as .prm, .pdb and .itp ?

Thanks in Advance

hi

I wanted to calculate Life-Time H-Bond I wanted to calculate the H-Bond Life-Time like this table in this article

I kindly beseech your counsel and guidance in navigating this endeavor.

Hello all.

I need to calculate the average structure of a protein from a 100ns trajectory. I came across two commands - gmx cluster and gmx covar. I tried gmx clusters, but the structure I got at the end of the run is physically not correct. When I tried gmx covar it does provide an average structure, but the problem it starts Diagonalizing the covariance matrix, which is very costly. Can anyone suggest me how to deal with this problem ?

How does this average structure calculation work for these two commands ?

Can I stop running the gmx covar command after getting the average structure without the Diagonalizing part ?

Thank you so much.

I want to perform a MD simulation in LAMMPS for a water droplet impacting a rough Copper surface at an assigned velocity and then nucleate this droplet into ice.

I have made the droplet structure and the substrate surface individually using ATOMSK. I'm able to equilibrate the structures in LAMMPS individually as well - both at 250K which is the target temperature. However, the output from the two equilibration (droplet and copper substrate) yields two data files using the "write_data" command that need to be combined in order to obtain the final system.

My query is on what will be the best technique to merge these data files for a final equilibrated structure that can be used in LAMMPS. Any help or insight is appreciated.

I came across a manuscript under review titled “Neighbor List Artifacts in Molecular Dynamics Simulations”. see "Neighbor List Artifacts in Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage" This study claimed that many non-expert users rely on default values for key inputs, which can lead to deformation in some cases, such as large membranes simulations. The study also suggested that most simulations suffer from inappropriate parameters for outer cutoff, ri and nstlist, resulting in missing long-range Lennard-Jones interactions. I would appreciate any comments and suggestions.

Hello,

I measured the distance between two centers of mass during a MD run using gmx distance. Even though the -oall file shows me that the distance changed over time the histogram file -oh puts 100% of probability on the last bin.

As this makes no sense does anyone have an idea on what happened?

Both files are attached

Thank you very much in advance and have a nice day!

i have done md simulation with gromacs software but when i check the trajectories with vmd their is a break in dna strand even after repeated simulation with ligand? what will be the possible reason for this.

For an amino acid of size around 1000 aa, during the energy minimization step, I am not able to go beyond because it shows, "segmentation core dump", I have tried sudo get update and sudo clean all command to clear the cache memory, but nothing works.

Could someone please help me out with solving it via any other actions?

Hello all.

I need to calculate the average structure of a protein from a 100ns trajectory. I came across two commands - gmx cluster and gmx covar. I tried gmx clusters, but the structure I got at the end of the run is physically not correct. When I tried gmx covar it does provide an average structure, but the problem it starts Diagonalizing the covariance matrix, which is very costly. Can anyone suggest me how to deal with this problem ?

How does this average structure calculation work for these two commands ?

Can I stop running the gmx covar command after getting the average structure without the Diagonalizing part ?

Thank you so much.

hi

I wanted to draw diagram "Probability distribution of distance of drug from b-CD with gromacs"

I kindly beseech your counsel and guidance in navigating this endeavor.

pHello!

I have run a 100ns trajectory of membrane protein and small molecule using gromacs software with CHARMM36 force field, and then I wanted to calculate ligand binding energy using gmx_MMPBSA.

The command is "gmx_MMPBSA -O -i mmpbsa.in -cs full_0ns_protein_nolp.pdb -ci index_mod_gromacs.ndx -cg 1 14 -ct full_fit_100ns_nolp.xtc -cp topol_pro.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -deo FINAL_DECOMP_MMPBSA.csv".

However, there is an error as following "ImportError: dynamic module does not define module export function (PyInit_MPI)"

How to solve this?

Thank you！

I have a system described below

cation.pdb

anion.pdb

cation.mol2

anion.mol2

(cation+anion).pdb (300 each obtained from packmol)

frcmod.anion

frcmod.cation

How can I obtain (cation+anion).prmtop and (cation+anion).inpcrd of Amber and convert them into Gromacs format.

Thanks, in anticipating your kind responds.

I have been using PRODRG for small molecules topology for years, but now I can't access it, I have emailed its developers but couldn't get any response. I want to use Gromacs forcefield, so I have only 2 options, one is ATB which is not free for new molecules, and another one was PRODRG. Kindly give me suggestions if you know any other way. I have tried Swissparam and switched to Charmm ff but it also didn't work and gave me errors with LJ and at the energy minimization step.

Is it possible to use Acetonitrile as solvent for Molecular Dynamics simulation in GROMACS or DESMOND?

hi all ,

I am a beginner in MD simulation and MD data analysis process so I just want to know what are the commands (orders)/ steps that I have to use to do PCA in right way

knowing that I am using Gromacs Software

thank you .

I submited the lig_fix.mol2 file to genarate topology into a str file and got this messege error:

"readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG ... attype warning: unknown sulfur type not supported; skipped molecule."

Hello all,

I am doing molecular dynamics simulation using gromacs for protein-ligand interaction. The simulation is going well. However, the crystal structure of protein have ANISOU instead of ATOM (shown in figure below). I wonder whether I need to rerun the simulation after remove the ANISOU from PDB.