Molecular Dynamics - Science topic

Hello, I'd like to perform quantum molecular dynamics simulation of a system of an electron and a chiral molecule and study the spin polarization. What molecular dynamics code is good for the task?

Dear all,

I'm simulating the CO2 adsorption on two graphite sheets using the LAMMPS software and I calculated the density profiles in the pore width. Now I would like to compare the results with some experimental values. In the laboratory I obtained the quantities adsorbed as mmol/grams of adsorbent.

Do any of you know how to calculate the same quantities starting from the density profile of LAMMPS?

Thank you in advance,

Beatrice

I need to calculate the molecular dynamics of the interaction of quercetin and isorhamnetin with neuraminidase

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 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.

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 teach computational chemistry to elementary students and I should explain this difference with basic words.

""DFT 🆚 MD""

I want to analyze the biomedical properties of green synthesized nanoparticles.

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.

I studied the properties of W-Cu alloys using molecular dynamics simulation,well I didn't find the eam potential of W-Cu alloy, How can I get or fit the potential for my simulation work ?Thank for your answer

Hí, could someone help me? I want to use the GPUs of my graphics card. I use windows 10 and performed molecular dynamics with NAMD2 with Charmm Gui. How can I activate the GPUS. I have this equipment AMD Ryzen 9 7900 12-Core Processor 3.70GH GEFORCE RTX 3060 RAM 32.0GB

What are the advantages of doing this, against doing just the molecular dynamics? what aditional information is the docking giving me, that the molecular dynamicsis not?

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.

Recently I have done SASA ( Solvent Accessible Surface Area) analysis for one of my research. But I have found some high fluctuations in SASA diagram which are actually 5 times higher than the unbound forms. My question is why do we find such fluctuations or spike in SASA diagram?

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."

Greetings great scholars.

I am new to molecular dynamics simulation. I am studying the solvation dynamics of a terpolymer optimized in four solvents; dmso, ethanol, methanol, and water. I presented the results using the following parameters: total energy, potential energy, kinetic energy, and the temperature

With my current knowledge of solvation dynamics, my aim in the present study was to estimate the stability and adsorption of the solvents. Through this, I am interested in knowing the parameters to consider before establishing the most stable solvent. I'm thinking of concluding using the final total energy. Based on my knowledge, lower total final energy is accounted for higher solvent stability and the other way around. I will be glad if a scholar here explains this better for me.

Thank you all.

~Daniel AGUROKPON

I am preparing to conduct shock simulation for an energetic material in LAMMPS with the help of a classical forcefield. How can I apply shock absorbing boundary condition so that that I can gather information during shock properly?

Hello every one, I am using Charm-gui for molecular dynamics While i am uploading the protein complex in solution builder "Error parsing HETAT, expected chain ID at column 22, but got '': HETATM 1 C. Please help me to troubleshoot. Thank you

Hi, I am working on protein-protein interaction studies, specifically on antibody-antigen interaction.

Hi

I am new to LAMMPS, and trying to learn how to simulate liquid molecular environments, I was looking for a way of generating input structure files, I've come across so many different software (such as vmd and its plugins which is not user friendly and was a waste of time), does anyone know any good tutorial to learn how to build such input file (if we don't use already available pdb files)? I am quite familiar with Gaussian, is there any way to get the structure of one molecule from the Gaussian and build the pdb file based on that? I understand that we probably need more than one molecule as the input molecular structure.

I ran a molecular dynamics simulation which was interrupted at the penultimate stage due to a power cut.

because the reproducibility of the molecular dynamics results quite changes because of initial velocities and other factors.

Hi

is there any way to extract intra-molecular distance distribution in a cluster of geometrically optimized cluster of molecules in Gaussian?

Hi,

How can i calculate the angular distribution of the angles between water molecule water and surface? surface during molecular dynamics simulation?

I did simulations by GROMACS, is it possible by GROMACS? or just need my own code?

I refer you to the attached files and this article

I need to store a large amount of MD simulation trajectories in a database that I can interact with using python. Do databases like this exist currently?

The following error is coming while performing Molecular Dynamics in gromacs while running cgenff script. Numpy and networkx are already installed. Kindly suggest resolve the error

The screenshot of the error is attached

Thank You

While I was trying to generate ligand topology using CGENFF, the penalty score exceeded 50 (parameter penalty 141; charge penalty= 56.475). how do I reparameterize to obtain acceptable penalty score range?

I am new in Molecular dynamic (MD) simulation and try to quickly acquire some radial distribution functions for liquid mixtures at different concentrations, what is the best software for that? Has anyone used XenoView and is its results reliable for publishing?

Hello, I am fairly new to gromacs and molecular dynamics. I want to simulate thiols for starters for some applications and I want to generate the topology file for thiol. I found the PDB and ITP files for sulfanyl from ATB -

and I tried to use ‘pdb2gmx’. I have read up on the documentation but I can’t get it to work. I am stuck on how to modify a forcefield or how to simply create a new one for the molecule. Any help on how to generate the topology and gro files would be appreciated. Thanks

I'm planning to do some molecular dynamic simulation with Gaussian, (trying to simulate the alignment of an ensemble of water molecules in the presence of strong field), can anyone please explain if that is possible with Gaussian?

Using 1 MPI thread

Using 8 OpenMP threads

WARNING: Using the slow plain C kernels. This should

not happen during routine usage on supported platforms.

Back Off! I just backed up em.trr to ./#em.trr.7#

Back Off! I just backed up em.edr to ./#em.edr.7#

Polak-Ribiere Conjugate Gradients:

Tolerance (Fmax) = 1.50000e+03

Number of steps = 5000000

F-max = 1.07138e+12 on atom 1627

F-Norm = 2.29910e+10

Step 0, Epot=3.230856e+09, Fnorm=4.819e+09, Fmax=1.394e+11 (atom 1643)

Step 1, Epot=2.299594e+09, Fnorm=3.046e+09, Fmax=8.879e+10 (atom 1643)

Step 2, Epot=1.871346e+09, Fnorm=2.331e+09, Fmax=6.698e+10 (atom 1643)

Step 3, Epot=1.374672e+09, Fnorm=1.549e+09, Fmax=4.331e+10 (atom 1643)

Step 4, Epot=1.059982e+09, Fnorm=1.108e+09, Fmax=3.054e+10 (atom 1643)

Step 5, Epot=7.814666e+08, Fnorm=7.504e+08, Fmax=2.020e+10 (atom 1643)

Step 6, Epot=5.834828e+08, Fnorm=5.244e+08, Fmax=1.406e+10 (atom 1643)

Step 7, Epot=4.235868e+08, Fnorm=3.567e+08, Fmax=9.443e+09 (atom 1643)

Step 8, Epot=3.070316e+08, Fnorm=2.432e+08, Fmax=6.435e+09 (atom 1643)

Step 9, Epot=2.194594e+08, Fnorm=1.627e+08, Fmax=4.227e+09 (atom 1643)

Step 10, Epot=1.570532e+08, Fnorm=1.087e+08, Fmax=2.774e+09 (atom 1643)

Step 11, Epot=1.119821e+08, Fnorm=7.208e+07, Fmax=1.773e+09 (atom 1643)

Step 12, Epot=8.002037e+07, Fnorm=4.794e+07, Fmax=1.134e+09 (atom 1643)

Step 13, Epot=5.708226e+07, Fnorm=3.183e+07, Fmax=7.144e+08 (atom 1643)

Step 14, Epot=4.074676e+07, Fnorm=2.115e+07, Fmax=4.542e+08 (atom 1247)

Step 15, Epot=2.909117e+07, Fnorm=1.401e+07, Fmax=2.946e+08 (atom 1247)

Step 16, Epot=2.083233e+07, Fnorm=9.278e+06, Fmax=1.905e+08 (atom 1247)

Step 17, Epot=1.496813e+07, Fnorm=6.147e+06, Fmax=1.226e+08 (atom 1247)

Step 18, Epot=1.079560e+07, Fnorm=4.084e+06, Fmax=7.859e+07 (atom 1247)

Step 19, Epot=7.805438e+06, Fnorm=2.721e+06, Fmax=5.010e+07 (atom 1247)

Step 20, Epot=5.652430e+06, Fnorm=1.817e+06, Fmax=3.217e+07 (atom 1029)

Step 21, Epot=4.095803e+06, Fnorm=1.215e+06, Fmax=2.188e+07 (atom 1029)

Step 22, Epot=2.968536e+06, Fnorm=8.135e+05, Fmax=1.481e+07 (atom 1029)

Step 23, Epot=2.150422e+06, Fnorm=5.451e+05, Fmax=9.952e+06 (atom 1029)

Step 24, Epot=1.555052e+06, Fnorm=3.658e+05, Fmax=6.630e+06 (atom 1029)

Step 25, Epot=1.119857e+06, Fnorm=2.462e+05, Fmax=4.383e+06 (atom 1029)

Step 26, Epot=7.993461e+05, Fnorm=1.666e+05, Fmax=2.882e+06 (atom 1029)

Step 27, Epot=5.598636e+05, Fnorm=1.138e+05, Fmax=1.893e+06 (atom 1029)

Step 28, Epot=3.774210e+05, Fnorm=7.828e+04, Fmax=1.247e+06 (atom 1029)

Step 29, Epot=2.369534e+05, Fnorm=5.399e+04, Fmax=8.796e+05 (atom 744)

Step 30, Epot=1.289057e+05, Fnorm=3.717e+04, Fmax=6.107e+05 (atom 744)

Step 31, Epot=4.626921e+04, Fnorm=2.549e+04, Fmax=4.173e+05 (atom 983)

Step 32, Epot=-1.642341e+04, Fnorm=1.744e+04, Fmax=2.799e+05 (atom 983)

Step 33, Epot=-6.411712e+04, Fnorm=1.201e+04, Fmax=1.837e+05 (atom 983)

Step 34, Epot=-1.013353e+05, Fnorm=8.406e+03, Fmax=1.188e+05 (atom 983)

Step 35, Epot=-1.313058e+05, Fnorm=5.950e+03, Fmax=8.340e+04 (atom 1247)

Step 36, Epot=-1.558091e+05, Fnorm=4.232e+03, Fmax=5.867e+04 (atom 1247)

Step 37, Epot=-1.759417e+05, Fnorm=3.002e+03, Fmax=4.576e+04 (atom 1247)

Step 38, Epot=-1.921374e+05, Fnorm=2.096e+03, Fmax=2.971e+04 (atom 1247)

Step 39, Epot=-2.045221e+05, Fnorm=1.501e+03, Fmax=2.753e+04 (atom 1247)

Step 40, Epot=-2.128392e+05, Fnorm=2.220e+03, Fmax=8.603e+04 (atom 707)

Step 41, Epot=-2.130309e+05, Fnorm=2.132e+03, Fmax=8.083e+04 (atom 707)

Step 42, Epot=-2.134006e+05, Fnorm=1.881e+03, Fmax=6.584e+04 (atom 707)

Step 43, Epot=-2.147213e+05, Fnorm=3.070e+03, Fmax=1.144e+05 (atom 708)

Step 44, Epot=-2.147343e+05, Fnorm=3.101e+03, Fmax=1.136e+05 (atom 708)

Step 45, Epot=-2.191163e+05, Fnorm=9.878e+02, Fmax=3.092e+04 (atom 1343)

Step 46, Epot=-2.199840e+05, Fnorm=8.657e+02, Fmax=1.976e+04 (atom 1343)

Step 47, Epot=-2.210286e+05, Fnorm=7.453e+02, Fmax=1.078e+04 (atom 1343)

Step 48, Epot=-2.223372e+05, Fnorm=6.792e+02, Fmax=7.796e+03 (atom 1247)

Step 49, Epot=-2.241242e+05, Fnorm=6.127e+02, Fmax=6.994e+03 (atom 1247)

Step 50, Epot=-2.264262e+05, Fnorm=5.402e+02, Fmax=5.626e+03 (atom 1247)

Step 51, Epot=-2.292161e+05, Fnorm=4.638e+02, Fmax=3.997e+03 (atom 744)

Step 52, Epot=-2.323968e+05, Fnorm=4.285e+02, Fmax=9.020e+03 (atom 707)

Step 53, Epot=-2.335971e+05, Fnorm=4.262e+02, Fmax=1.052e+04 (atom 708)

Step 54, Epot=-2.366034e+05, Fnorm=6.558e+02, Fmax=2.801e+04 (atom 708)

Step 55, Epot=-2.407879e+05, Fnorm=2.008e+03, Fmax=8.592e+04 (atom 707)

Step 56, Epot=-2.409638e+05, Fnorm=1.915e+03, Fmax=7.883e+04 (atom 707)

Step 57, Epot=-2.426413e+05, Fnorm=7.860e+02, Fmax=3.555e+04 (atom 1441)

Step 58, Epot=-2.443507e+05, Fnorm=3.451e+02, Fmax=6.412e+03 (atom 1441)

Step 59, Epot=-2.455093e+05, Fnorm=2.703e+02, Fmax=4.863e+03 (atom 1639)

Step 60, Epot=-2.466843e+05, Fnorm=5.576e+02, Fmax=2.309e+04 (atom 1642)

Step 61, Epot=-2.471133e+05, Fnorm=9.062e+02, Fmax=4.381e+04 (atom 1639)

Step 62, Epot=-2.472244e+05, Fnorm=3.280e+02, Fmax=1.020e+04 (atom 1627)

Step 63, Epot=-2.476386e+05, Fnorm=3.163e+02, Fmax=1.049e+04 (atom 1627)

Step 64, Epot=-2.481261e+05, Fnorm=2.894e+02, Fmax=9.361e+03 (atom 1627)

Step 65, Epot=-2.483511e+05, Fnorm=3.638e+02, Fmax=1.392e+04 (atom 1627)

Step 66, Epot=-2.483752e+05, Fnorm=5.857e+02, Fmax=2.356e+04 (atom 1627)

Step 67, Epot=-2.493838e+05, Fnorm=2.743e+02, Fmax=7.574e+03 (atom 1643)

Step 68, Epot=-2.496374e+05, Fnorm=1.567e+02, Fmax=1.829e+03 (atom 1639)

Step 69, Epot=-2.498764e+05, Fnorm=1.598e+02, Fmax=3.421e+03 (atom 1431)

Step 70, Epot=-2.502622e+05, Fnorm=2.798e+02, Fmax=1.309e+04 (atom 1431)

Step 71, Epot=-2.538323e+05, Fnorm=1.717e+03, Fmax=8.681e+04 (atom 1432)

Step 72, Epot=-2.542346e+05, Fnorm=1.691e+03, Fmax=8.526e+04 (atom 1432)

Step 73, Epot=-2.549277e+05, Fnorm=1.715e+03, Fmax=8.647e+04 (atom 1429)

Step 74, Epot=-2.550878e+05, Fnorm=1.643e+03, Fmax=8.270e+04 (atom 1432)

Step 75, Epot=-2.550992e+05, Fnorm=1.716e+03, Fmax=8.645e+04 (atom 1429)

Step 76, Epot=-2.551361e+05, Fnorm=1.637e+03, Fmax=8.236e+04 (atom 1432)

Step 77, Epot=-2.551654e+05, Fnorm=1.714e+03, Fmax=8.634e+04 (atom 1429)

Step 78, Epot=-2.551766e+05, Fnorm=1.636e+03, Fmax=8.234e+04 (atom 1432)

Step 79, Epot=-2.552027e+05, Fnorm=1.679e+03, Fmax=8.504e+04 (atom 1429)

Step 80, Epot=-2.552057e+05, Fnorm=1.627e+03, Fmax=8.172e+04 (atom 1432)

Step 81, Epot=-2.552060e+05, Fnorm=1.710e+03, Fmax=8.619e+04 (atom 1429)

Step 82, Epot=-2.552060e+05, Fnorm=1.639e+03, Fmax=8.260e+04 (atom 1432)

Energy minimization has stopped, but the forces have not converged to the

requested precision Fmax < 1500 (which may not be possible for your system).

It stopped because the algorithm tried to make a new step whose size was too

small, or there was no change in the energy since last step. Either way, we

regard the minimization as converged to within the available machine

precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not

needed for preparing to run molecular dynamics.

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.7#

Polak-Ribiere Conjugate Gradients converged to machine precision in 82 steps,

but did not reach the requested Fmax < 1500.

Potential Energy = -2.5520603e+05

Maximum force = 8.2601156e+04 on atom 1432

Norm of force = 1.6394663e+03

Hi ,I am working on cysteine adsorption Au surface so i am tried to energy minimisation it giving this error again and again energy minimisation has stopped,i tried everything changing integrator, to emtol,rvdw still error has occuring. Pls help me I am stuck for a long time,dont know whats getting error.

and If i am proceeding with this ,in nvt i am getting lincs warning

Dear all Gromacs user, I am using Gromacs to run NVT and NVT equilibrium.

Before the equilibrium, my input gro file shows all atoms (proteins, Zn, Na and Cl ions, and waters) stayed in the box with the periodic condition.

But after equilibrium, the protein itself shows no periodic condition, which means some parts of it are out of box, while otehr atoms remain periodic condition.

I check via VMD and found there are several Zn stay in the box but the protein residues binding with them are out of the box.

How can I fix this? I need Zn stay in Zn-binding domain with the protein whole (not cut by the box).

I am going to run a longer MD. Or this sitiuation won't affect the following MD actually so I don't need to wooried about this?

The screenshot of VMD result was attached.

How can I download DESMOND for molecular dynamics analysis from the website: https://www.deshawresearch.com/downloads/download_desmond.cgi/ ?

I have already tried filling out the form and so far I can't access the download link or receive any link by email. Has anyone had the same problem?

Hi,

recently I made the file in the attachments. I would like to do the same again but I forgot how to do it. I've already tried downloading the OUTCAR and CHGCAR file from my MD simulation, but when I open the file I get an empty box as output. Is there anyone how to create this figure? It shouldn't be too hard I guess.

Thanks in advance,

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

Is there a tutorial or a paper that decsribes how to perform principal component analysis using GROMACS and how to interpret the data obtained?

Chromium layer deposited on fused silica substrate should technically react with oxygen dangling bonds of fused silica. The adhesion of film to the substrate is dictated by strength of the bond, which intrinsically depends on type of oxide formed CrnOm, the values of n and m. I want to determine n,m using molecular dynamics or DFT.

Hello everyone. I'm new to molecular dynamics and don't have enough knowledge of LAMMPS. I want to do a tensile test of graphene - GaN nanosheet. I have the data file of the sheet and I'm using tersoff potential. Can anyone help me with any resource on creating the input file? I've seen the lammps online documentation but it was only done for a single material. Thanks.

I have ran a MDS for variants of the same protein docked to the same receptor, yet there is 2 complexes that has an outlying values regarding (Van der Waal, electrostatic energy, and importantly binding affinity)

- could it be related to a fault within the MDS procedure?

Running MD simulation , NVT equilibrium, on google colab , some restarts are required due to time limitation of the server. I wonder if there is a way to find out how many steps are left to completed version of the output file , out of whole steps that are set by ((.mdp)) file.

Can someone please list the analysis that needs to be performed to understand and compare the mechanism of a protein in its native and inhibitor-bound state? (NOTE: Not the interaction between Protein and Ligand)

Are there free databases of peptides?

What is the best and software for AISMD?

I found named Tera Chem. Please share your views regarding this software. Please suggest

Hi,

Imagine that you are going to sample a protein conformation (consists of N atoms) using Monte Carlo and Molecular Dynamics simulations, independently.

For the MD simulation, the phase space has a dimension of 6N dimension (3N position and 3N momentum). I'm assuming that the phase space for MC has a dimension of 3N (just position of atoms). Am I missing something here?

Hi,

I am new to gromacs and using gromacs 4.6.5 and dssp-2.0.4. To study the secondary structure, when I am running these commands:

>export DSSP=/usr/local/bin/dssp

>do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp.xvg -ver 2

I am getting this error:

dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2> /dev/null' Reading frame 0 time 0.000 Back Off! I just backed up dd31ZWbc to ./#dd31ZWbc.1#

-------------------------------------------------------Program do_dssp, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_do_dssp.c, line: 669

Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option.

I have already checked many helping sites but couldn't solve it.

I don't know how to fix it. Please help me?

I am working on molecular dynamics of polymers. With the available softwares like molveiw, gaussian, there are limitations to how big molecules can be built. I was able to build a hexamer of hyaluronic acid, but I need at least a 100mer of the same molecule for simulation. Can anyone please help me with how to build long chain polymer and parametrize them?

Kind regards.

I want to do molecular dynamics simulation of polymers. The polymer is composed of monomers and the monomers have different type of epimers. Is molecular dynamics able to reveal the difference between polymers consisting of different monomers? Or are they completely the same thing in the view of molecular dynamics?

For example, the monomer could be β-D-glucopyranose or β-D-mannopyranose. If the first molecule is built with solely β-D-glucopyranose, the second molecule is built with solely

β-D-mannopyranose, and the third molecule is built with a random combination of the two monomers. In molecular dynamics simulation, is the difference between the three molecules could be revealed?

The difference of β-D-glucopyranose and β-D-mannopyranose can be found at this Wikipedia link https://en.wikipedia.org/wiki/Epimer?oldformat=true

Any help would be much appreciated!

I ran a MD simulation for 30 ns using Amber99ff ILDN for protein forcefield and GAFF for ligand forcefield for GKRP and F1P (PDB: 4BB9) consecutively. However, the result shows that the RMSD Complex fluctuates over time until it reach about 27 ns. Also, the RMSD score varies between 50-100 A which very high RMSD score.

Thank you in advance.

Hey everyone,

The authours of an article have been performed Molecular Dynamcis Simulations (MDS) using Amber and they extracted different conformations (31 conf.), and it seems like Amber is not free. So instead I use Gromacs but I didn't know how to extract various conformation of my peptide. So is it even possible to do the same using Gromacs or not ? and how ?

MD simulation of a protein complex with more than 600 AA residues shows an average rmsd between 1-1.5 nm. can the protein complex can be considered stable?

Besides sometimes i see a jump in the RMSD trajectories. Can it be arised due to the failure to centre the protein complex or due to the larger size of the protein.

In order to determine the nucleation rate J, using MD simulations by following the mean first passage time (MFPT) technique, it is necessary to determine the size of the largest cluster of atoms formed (n) over the time period of the simulation (Tn). The mean first-passage time for each size (n) is simply obtained by averaging (Tin) over several repetitions of the simulations with different initial configurations.

Could anyone kindly highlight or provide insight on how this can be achieved in LAMMPS or in general in any MD software package? Thanks.

I am working with an energetic material. using a classical forcefield how can I calculate isothermal compressibility by volume fluctuation formula, and coefficient of thermal expansion by the enthaply-volume fluctuation formula for a solid in LAMMPS?

Hi!

I am analyzing the trajectory (generated with Desmond) of a protein simulated in periodic boundaries conditions. In some frames, as you can see from the figure, data are clearly altered due to the mirroring of a portion of one chain on the opposite side of the box. I tried to center the trajectory with a specific script, but nothing changed. Is there a way to fix this?

I'm trying to get parameters from CGENFF for FAD molecule. It has -2 charge that lies on two O atoms.

Error generated is:

readmol2 warning: non-unique atoms were renamed. Now processing molecule ***** ... attype warning: carbon radical, carbocation or carbanion not supported; skipped molecule.

I have also attached my molecule in mol2 format.

Thank you

I had developed a homology modeled protein and identified the cavity of the protein through bioinformatic software. unfortunately, i couldn't calculate the cavity volume in my modeled protein. I want to get some information about the cavity volume and size in modeled protein for de novo drug design. kindly let me know the way to calculate the cavity volume of the homology modeled protein

to do molecular dynamics for a protein with online tool

Dear experts

I am a fresher for molecular dynamics and simulation studies. Kindly suggest me some tutorials for the same. It would be nicer if you drop your picks for open acess MD simuation softwares.

Thank you in anticipation.

I have performed MD simulation of 100ns on Desmond and now I want to calculate solvent accessible surface (SASA) area over the trajectory. Can Anyone please guide how to do it? Thanking you all in Anticipation.

Dear,

I want to perform a Molecular Dinamics simulation in a protein with 5 molecules of NAG attached to it.

Since the covalent bond between the carbohydrate and the protein creates an unusual bond, the GROMACS page shows that I should change something in the specbond.dat, but nothing more...

Are there any tutorials explaining how to prepare the system to perform the simulation using the GROMACS software (or could someone explain)?

Thanks for your help.

Is it hard to learn Molecular dynamics (MD) simulation? Do you have a suggestion for learning?

I had ran molecular dynamic simulation on apo protein using TIP3P, TIP4P, TIP4PEW and SPC for 25 ns to establish the most suitable solvent model for specific protein. However, none of them gave low RMSD value. The lowest RMSD value is between 3.0 - 3.5 for TIP3P. But when I ran the protein with the ligand, the RMSD value become higher around 3-4. So what other parameter that I need to consider to establish the model?

I have performed molecular dynamics of RNA using NAMD (v.2) now I have both the PDB of the water-solved system and the DCD file. Does anybody know how to extract the RMSF data in VMD? Are there codes that I have to type in the Extensions>TK Console, or are there procedures that I have to do in Extensions>Analysis>Timeline (I tried using this but error)?

Thank you

After equilibrating structure at 600K by Molecular Dynamics, can we find out equilibrium crystal shape by Wulff construction.

I have the cif file of Dihydroxylammonium-5,5'-bistetrazolyl-1,1'-diolate (tkx-50). I want to run Molecular dynamics simulation of TKX-50, for which I need to prepare a lammps data file with all the angles, dihedrals, and impropers being defined. I tried to convert the cif file to lammps data file by Openbabel, however, the output was not appropriate. In the unit cell there are supposed to be two molecules with 48 atoms. Whereas in different softwares different numbers of atoms are appearing using the same cif file. Say, in vesta it shows 98 atoms. Can anybody guide me the way to prepare a perfect lammps data file of TKX-50 from it’s cif file?

I need to create a block of TiO2 in the anatase form to be used in Molecular Dynamics (MD). Can anyone help me out? I'm using LAMMPS as the MD package.

Thank you.

Chamara Somarathna

I am searching for any resources/guidance on the question above as the literature I have found seems to be on protein docking between two helical transmembrane proteins. I am attempting to perform a protein docking simulation in which one protein is in a membrane with extracellular components and the other is extracellular. As of now I have used NAMD/VMD for basic MD work. Any help is appreciated.

Hi All,

I am currently trying to make a solvent box with dichloromethane, which can then be used to solvate a solute I am working with.

For that, I embedded 1050 dichloromethane (DCM) molecules into a 5x5x5 nm box. The force field I am using is OPLS-AA. Energy minimization and NVT equilibration results look good. However, when I conduct the NPT equilibriation step, I run into the problem that the density of my dichloromethane box is given as 1.53 g/cm^3, which is quite far off the literature value of 1.33. I used the npt.mdp file from the well-known lysozyme tutorial (http://www.mdtutorials.com/gmx/), and ran it for a bit longer (1 ns), while changing the isothermal compressibility from 4.5e-5 (water) to 1.02e-4 bar^-1 (dichloromethane). I’ve attached the .mdp file.

Interestingly, when I look another DCM box (OPLS-UA forcefield) that has been made available through user contributions on the gromacs homepage (https://www.gromacs.org/user_contributions.html#:~:text=20%20May%202003-,ch2cl2_box.tgz,-The%20package%20contains), they used the isothermal compressibility value for water (!) and arrive at a dichloromethane density close to literature value. I did the same for my dichloromethane box and also arrive at a density of 1.34 g/cm^3, which is very close to literature. But surely there must be something wrong, with this, as I assume I can’t just swap compressibility values between compounds.

Is the higher density obtained with the dichloromethane compressibility much of an issue for further simulations? If so, what could be the problem with using the correct compressibility that causes the density to increase so much and is there a way to fix it?

I've attached the .mdp and files of my NVT equilibrated box.

Thank you all in advance! I appreciate any help with this issue, as I am fairly new in the field!

Kind Regards,

Nick

Suppose we have do MD calculation for structure at 800°C. Now can we do electronic structure calculation for that final MD structure but taking the optimized structure from LAMMPS and putting it as POSCAR file in VASP? I suppose DFT calculation minimization algorithm is built for 0K structure. So I am not sure that will it work or not.

I am using a Windows 10 computer and the new 64bit version of VMD for Windows (1.9.4). I would like to use the CaFE plugin to calculate the free binding energy of a protein-protein complex that I ran a 20ns simulation for using NAMD. I have been trying to use the plugin for several weeks now, but cannot get it to work properly.

I have created a script to run the CaFE plugin according to the template in the manual:

````

package require cafe 1.0

mmpbsa -top J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/protein.psf \

-trj J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/MD_20stride_protein.dcd \

-out mmpbsa.log \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_carb.prm \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_cgenff.prm \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_lipid.prm \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_na.prm \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_prot.prm \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/toppar_all36_carb_glycopeptide.str \

-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/toppar_water_ions_namd.str \

-com "segname AP1 CP1" \

-rec "segname AP1" \

-lig "segname CP1" \

-first 0 \

-last -1 \

-stride 10 \

-mm 1 \

-pb 1 \

-pb_exe C:/Users/Christos/Downloads/delphicpp_v8.4.4_windows_x64.exe \

-pb_rad mparse \

-sa 1 \

-sa_rad mparse \

quit

````

If I run this script in the VMD TK console with source script_name.vmd, the following prints in the TK console:

````

CaFE) Sanity check

CaFE) Found 5508 atoms for complex

CaFE) Found 4646 atoms for receptor

CaFE) Found 862 atoms for ligand

CaFE) Loaded 10000 frames for complex

CaFE) Generating new trajectory for complex

CaFE) Loaded 10 frames for complex

CaFE) It took 0 days 0 hrs 15 min 52 sec

CaFE) Calculating the MM term

CaFE) It took 0 days 0 hrs 0 min 33 sec

CaFE) Calculating the PB term

Info) ======================

Info) Please cite TopoTools as:

Info) Axel Kohlmeyer & Josh Vermaas, (2019). TopoTools: Release 1.8

Info) https://doi.org/10.5281/zenodo.598373

Info) ======================



````

In the VMD console, this is printed:

````

vmd > {C:\Users\Christos\Downloads\CaFE_Plugin-master\CaFE_Plugin-master\cafe1.0} {C:/Program Files/VMD/scripts/tcl8.6} {C:/Program Files/VMD/scripts} {C:/Program Files/lib} {C:/Program Files/VMD/scripts/tk8.6} {C:/Program Files/VMD/scripts/tk8.6/ttk} {C:/Program Files/VMD/scripts/vmd} {C:/Program Files/VMD/plugins/WIN64/tcl} {C:/Program Files/VMD/plugins/noarch/tcl} {C:/Program Files/VMD/plugins/noarch/tcl/tablelist6.11/scripts} c:/Users/Christos/Documents/vmdStore

psfplugin) Detected a Charmm PSF file

Info) Using plugin psf for structure file C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/Morikis_Non_PDBFix_20ns_Test4_QwikMD.psf

Info) Analyzing structure ...

Info) Atoms: 44191

Info) Bonds: 31315

Info) Angles: 22978 Dihedrals: 14830 Impropers: 957 Cross-terms: 348

Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0

Info) Residues: 13295

Info) Waters: 12870

Info) Segments: 11

Info) Fragments: 12945 Protein: 2 Nucleic: 0

dcdplugin) detected standard 32-bit DCD file of native endianness

dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)

Info) Using plugin dcd for coordinates from file J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/MD.dcd

Info) Coordinate I/O rate 10.5 frames/sec, 5 MB/sec, 950.4 sec

Info) Finished with coordinate file J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/MD.dcd.

Info) Opened coordinate file _mmpbsa_com_tmp.dcd for writing.

Info) Finished with coordinate file _mmpbsa_com_tmp.dcd.

psfplugin) Detected a Charmm PSF file

Info) Using plugin psf for structure file C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/Morikis_Non_PDBFix_20ns_Test4_QwikMD.psf

Info) Analyzing structure ...

Info) Atoms: 44191

Info) Bonds: 31315

Info) Angles: 22978 Dihedrals: 14830 Impropers: 957 Cross-terms: 348

Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0

Info) Residues: 13295

Info) Waters: 12870

Info) Segments: 11

Info) Fragments: 12945 Protein: 2 Nucleic: 0

dcdplugin) detected standard 32-bit DCD file of native endianness

dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)

Info) Using plugin dcd for coordinates from file _mmpbsa_com_tmp.dcd

Info) Finished with coordinate file _mmpbsa_com_tmp.dcd.

Info) Opened coordinate file com_mm_tmp.pdb for writing.

Info) Finished with coordinate file com_mm_tmp.pdb.

Info) Opened coordinate file rec_mm_tmp.pdb for writing.

Info) Finished with coordinate file rec_mm_tmp.pdb.

Info) Opened coordinate file lig_mm_tmp.pdb for writing.

Info) Finished with coordinate file lig_mm_tmp.pdb.

````

Checking the files in the working directory, the only new files created are _mmpbsa_com

_tmp.dcd, com_pb_tmp_0.delphi, com_pb_tmp_0.log, and com_pb_tmp_0.pqr. Since the time is not printed for the PB calculation in the TK console, I believe there is some error in that step. This is what is in the com_pb_tmp_0.log file:

````

Time> Program started on 2022-7-13 at 18:22:0

______________________DelPhi C++ V. 8.4________________________

| |

| DelPhi Fortran program was originally developed in Barry Honig|

| lab to compute electrostatic potential and energies. The |

| current C++ version is object oriented code, capable of |

| performing the calculations in sequential, OpenMP and MPI |

| regimes and the MPI version utilizes distributed memory |

| technology. Particular novelty is the Gaussian-based smooth |

| dielectric function that accounts for heterogeneity of the |

| solute and solute-solvent interface. |

| |

| The following reference should be quoted if the use of Delphi |

| V. 8.0 results to a publication: |

| |

| Li, L.; Li, C. A.; Sarkar, S.; Zhang, J.; Witham, S.; |

| Zhang, Z.; Wang, L.; Smith, N.; Petukh, M.; Alexov, E. |

| Bmc Biophys 2012, 5. |

| |

| For questions and help, visit |

| http://compbio.clemson.edu/forum/ |

| or email to delphi@g.clemson.edu |

| |

| Jul 2018, by DelPhi Development Team |

| Chuan Li |

| Zhe Jia |

| Arghya Chakravorty |

| Shailesh K Panday |

|____________________ ________________________|

DelPhi C++ V. 8.4

Time> Program started on 2022-7-13 at 18:22:0