Molecular Dynamics - Science topic

In my only CPU system, 97834 atoms (100ns), it took 43 hours in total.

For Docking, MzDock and LightDock

For Simulations, MDsrv and MDWeb

You can try Supervised Molecular Dynamics (SuMD)

(SuMD enables the investigation of ligand–receptor binding events independently from the starting position, chemical structure of the ligand (small molecules or peptides), and also from its receptor-binding affinity.)

Regards

Even though it may not look like that to you, the calculations are actually based on the definition.

Now, about your proposed formulae: while in coarse, semiclassical approximation the internal energy could sort of be calculated in the proposed one-particle manner, in reality it is quantum mechanical and you can no longer simply break it down like that.

The entropy is an even bigger fish here: it cannot be divided into "one-particle contributions" like that, it has to be calculated via a partition function or something equivalent according to the quasi ergodic hypothesis (mean value over time = ensemble mean value).

Once you start calculating a partition function (or an equivalent) for the entropy, you get the internal energy "on the fly", so it makes no sense to use coarse approximations here, anyway.

Dear Muhammad Umar Khan Niazi ,

I am not familiar with your simulations;

but, nevertheless, I have the impression that there might be something wrong with your '2theta' axis...

You have a lot of peaks at the beginning of the pattern.

Perhaps you have a wrong wavelength number in use ('Angstrom' wrongly interchanged with 'nm' or vice versa) or wrong angular scale

Please check that...

Best regards

G.M.

Hello Syeda M Rizvi,

I wish you are doing well. I am dealing with MD Simulation and facing the same problem as you did. I wonder how did you solve this problem?

Thank you so much for your reply.

This might be helpful: https://github.com/lammps/lammps/blob/develop/examples/ELASTIC/in.elastic

Use GROMACS for the same

(https://www.gromacs.org/)

For plotting graphs n analysis you can use QTgrace.

Regards

NO,

if you have more funding, go for RTX 4090.

Thank you :) I did that, and it helped me!

What helped me is to manually delete atoms added by Amber from comp.pdb file produced at the following step:

The issue is now corrected, everything works fine.

Half a hour I experienced before (alomst 1000, molecular weigh), but this number shouldn't be the longest one.

Dear Gabriel Vinicius

Thank you very much for your answer.

Hello, Gayatri Madhukar Jejurkar Dr. Gayatri despite trying to reach you through your mail, I am unable to contact you or send any message to you. Please reach me

Dear Masoud Khajenoori

Thanks for your reply.

How have you modelled the metal ions bonded with protein for simulation?

Several free software packages are available for Molecular Dynamics (MD) simulations, each with different features and capabilities.

1. GROMACS

2. LAMMPS

3. NAMD

4. AMBER (AmberTools)

5. OpenMM

6. HOOMD-blue

7. CP2K

These tools cover a broad range of MD applications, from biomolecular simulations to materials science.

Aashish Bhatt , thank you for your response. I will certainly try this software and method.

maybe you can start with this one:

Thats right ,Its not related to the preparation of the molecule.

its meant for your gromacs MD ,you will use the coordinate of the prepared molecule and add its force field ,angles ..ect

If you are doing MD simulations, you are already probably using a supercell large enough to allow you to distribute atoms randomly or quasi-randomly over the shared sites, getting a better representation of the disordered system. VCA only makes sense, if it does at all, to force a small-cell calculation for a disordered system. For MD simulations, use an SQS supercell (this places the atoms in a way that mimicks the distribution functions of a truly disordered system). O, if you supercell is very large, just assign random occupations.

You can include this video and the references therein:

Once uoy have changed the name of N instaed of HETATM, how did you visualise the simulation part in VMD

Same Question

Thank you sir. You are lifesaver. Thank you so much sir.

Thank you Edward Francisco Méndez Otálvaro . I will certainly try this.

Greetings Orhan Kıbrıslı

I also have had problems with XTB, in my case, for calculations with Ti atoms. The structure would converge for unrealistic bond lenghts that would render the optimization impossible (something already known in the community for early transition metals). I don't know if there are similar problems for Li and Sb, but it might be possible.

I had more success using semi-empirical methods based on the Neglect of diatomic differential overlap (NDDO) for systems were DFT or Post-HF were not options.

Hope it helps.

Try doing with catdcd in namd

catdcd -o eq_all.dcd eq01.dcd eq02.dcd eq03.dcd

Hello,

I actually just run that command inside tleap before typing quit. That was the error for sure! I solved it some minutes ago. Now it works.

Thank you for your kind response

How did you decide how many ions to pack in a simulation box ?

Yes and no. There are minor differences which can cause your results to be false. Reducing the grid box would definitely decrease the total volume so that the interactions will increase just like in a more concentrated situation. However, when your ligand and/or receptor (target molecule) goes outside the walls of grid box, it comes back from the other side (Leaving the grid from right, entering from left etc...). So in that sense, you create a new collision probability for the atoms to interact. Let's assume you have a tiny drug that you want to bind to your large protein to inhibit/suppress its activity. In terms of theoretical chemistry, it may not have any chance to attack and residue on the right side of that protein. As you limit the grid-box, some right parts of that protein will enter from the left side and your drug will be able to interact that side as well which is not supposed to happen. So if you want to increase the concentration go ahead and do it. Please do not decrease the grid-box volume to satisfy that need since it will yield wrong outcomes.

If you don’t do it already I would take care that you calculate the free energy from a bunch of frames that represent different conformations of your structure. This will give you (hopefully) a more realistic estimation. good luck

Thank you so much! Your answer was very helpful for my research.

compute f1 poly CH2 force/tally BOR

variable fx equal c_f1[1]

variable fy equal c_f1[2]

variable fz equal c_f1[3]

fix ff poly ave/correlate 1 100 100 c_f1[1] c_f1[2] c_f1[3] type auto file force.dat ave running

I written these lines to extract force but im getting error

ERROR: Unrecognized compute style 'CH2' (src/modify.cpp:1282)

Last command: compute f1 poly CH2 force/tally BOR

where I did mistake Can you please help me out.

Dear@Ahmet Burak Yıldırım,

At the moment, I'm having a similar problem, and I'd like to ask how you ended up solving it, can you give me some advice, if I need to, I can upload my simulation file, I'm not doing water, I'm doing liquid alkanes, and I think there's a similari

1. Create an index file with the specific segment as a separate group. You can use the make_ndx command for this. If you want to create a group for residues 1 to 20:

$echo -e "r 1-20\nq" | gmx make_ndx -f md.gro -o index.ndx

This command will create a new group with residues 1 to 10 and save the index file as index.ndx.

2. Calculate the RDF using the gmx rdf command and specify the new group as one of the groups for which to calculate the RDF:

$echo -e "Group1\nGroup2" | gmx rdf -s md.tpr -f md.xtc -n index.ndx -o rdf.xvg

I hope someone finds this useful, I have myself been struggling with the same problem. My solution to this is looking at the chemical time and ns/day data, which is constantly updated.

To check this go to MONITOR -> double click running MD job -> check the last entry (status -running).

Double click the last entry for a 100ns default Simulation 100000 chemical time means 100ns this might give a rough idea of percentage job progress.

Going by the ns/day data can give you a rough idea of simulation speed like 11ns/day for 100ns simulation will finish on 10th day of the run applied.

Actually, I have worked on PEC and have also generated them. However, the thing is, in polyatomic molecules, we need to consider molecular dynamics. Once we scan a particular bond, the other bonds do not remain the same. So my worry is how we can incorporate this effect to obtain accurate PEC curves...

Jyri Kimari

i have attached this conversation link to the NAMD Mailing List with some details to make sure whether this method is usable or not.

As previously suggested, the PDB is a textual file. You can open it and make all the modifications you need. Be careful not to misalign the columns to avoid disrupting subsequent calculations.

If you have Gromacs installed, you can renumber the PDB file using the command: gmx editconf -f file.pdb -resnr starting_number -o output.pdb

Replace file.pdb with the name of your PDB file, starting_number with the desired starting number for residue numbering, and output.pdb with the desired output file name.

I tried filling the form thrice. Still couldn't get the download link. Also can you give more details on which upper part because the option for "already filled the form can't be seen".

How do we calculate the structure factor using Travis? Is there any specific way or command to calculate it@Mirella-Simoes-Santos

Thanks in advance.

Just from the nice pic, I think the data different between MD and exp. is fairly closed from my point.

A small tip is that in exp. materials often consist of defects, vacancies, dislocation, grain boundaries and so on but in MD the materials is a perfect crystal in your case.

So I think you can accept this result.

And if you're not satisfied, I would like to propose two aspects which you can do furhter tests.

1. increase the number of atoms in the system. A big system would result in better results( or not).

2. chose a "good" potential. A good potential is critical to the properties of systems. Before you do further production run, a systematical tets of exsists potentials is essential.

Okay! I'll do this.

$ cd ~

sudo apt-get install libnotify4 xdg-utils libxcb-dri3-0 libgbm1 libnss3 libgtk-3-0 libatspi2.0-0 g++

sudo apt -y install ncurses-term

$ cd ~/Downloads

wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/163da6e4-56eb-4948-aba3-debcec61c064/l_BaseKit_p_2024.0.1.46_offline.sh

sudo sh ./l_BaseKit_p_2024.0.1.46_offline.sh

$ apt install ocl-icd-libopencl1

$ cd ~/Downloads

mkdir neo

cd neo

wget https://github.com/intel/intel-graphics-compiler/releases/download/igc-1.0.15136.4/intel-igc-core_1.0.15136.4_amd64.deb

wget https://github.com/intel/intel-graphics-compiler/releases/download/igc-1.0.15136.4/intel-igc-opencl_1.0.15136.4_amd64.deb

wget https://github.com/intel/compute-runtime/releases/download/23.35.27191.9/intel-level-zero-gpu-dbgsym_1.3.27191.9_amd64.ddeb

wget https://github.com/intel/compute-runtime/releases/download/23.35.27191.9/intel-level-zero-gpu_1.3.27191.9_amd64.deb

wget https://github.com/intel/compute-runtime/releases/download/23.35.27191.9/intel-opencl-icd-dbgsym_23.35.27191.9_amd64.ddeb

wget https://github.com/intel/compute-runtime/releases/download/23.35.27191.9/intel-opencl-icd_23.35.27191.9_amd64.deb

wget https://github.com/intel/compute-runtime/releases/download/23.35.27191.9/libigdgmm12_22.3.11.ci17747749_amd64.deb

$ wget https://github.com/intel/compute-runtime/releases/download/23.35.27191.9/ww35.sum

sha256sum -c ww35.sum

$ sudo dpkg -i *.deb

# cd ~/

sudo git clone --recurse-submodules https://github.com/codeplaysoftware/syclacademy.git

$ cd ~/Downloads

wget ftp://ftp.gromacs.org/gromacs/gromacs-2023.3.tar.gz

tar xfz gromacs-2023.3.tar.gz

cd gromacs-2023.3

mkdir build

cd build

$ cd ~/syclacademy/External/Catch2/single_include/

cp -r catch2 ~/Downloads/gromacs-2023.3/build

cd ~/Downloads/gromacs-2023.3/build

ls

cd ~/syclacademy/Code_Exercises/Exercise_01_Compiling_with_SYCL

cp -r source.cpp ~/Downloads/gromacs-2023.3/build

cd ~/Downloads/gromacs-2023.3/build

ls

# withou exit the build directory activate the environment of one api using the following comand:

$ source /opt/intel/oneapi/setvars.sh

icpx -fsycl -I ~/syclacademy/External/Catch2/single_include -o a.out source.cpp

ls

# this should create a file called a.out in the build directory

cd ~/

sudo apt install gcc cmake libpomp-dev hwloc libhwloc-dev

cd ~/Downloads/gromacs-2023.3/build

$ sudo su

$ source /opt/intel/oneapi/setvars.sh

$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DGMX_GPU=SYCL -DGMX_HWLOC=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-23

$ make -j 8

$ make check

$ make install

1. open the work directory

2. run as root

3. open the intel environment with: $ source /opt/intel/oneapi/setvars.sh

4. activate gromacs with: $ source /opt/gromacs-23/bin/GMXRC

Dear Amol,

See the following link:

VESTA, LAMPS, GROMACS,NANOTUBE MODULER

I'm assuming bcc?

If you are talking about cumulative slip, then yes the cumulative slip will be {112} if you shear along a {112} plane. If you are talking about the fundamental slip behavior, then no, everything points to bcc screw dislocation slip being fundamental {110} steps with cross-slip to different planes. "True" {112} slip could be thermally activated at higher temperatures, but I'm not sure if it would be distinguishable from {110} zig-zag and the two would be in competition.

Also, with classic MD, be careful of the interatomic potential that you use as most will incorrectly predict the slip nature. You want a potential that predicts a compact (a.k.a. non-polarized) core and a single-humped Peierls barrier.

[1] C.R. Weinberger, B.L. Boyce, C.C. Battaile, Slip planes in bcc transition metals, International Materials Reviews 58(5) (2013) 296-314.

[2] L.M. Hale, J.A. Zimmerman, C.R. Weinberger, Simulations of bcc tantalum screw dislocations: Why classical inter-atomic potentials predict {112} slip, Computational Materials Science 90 (2014) 106-115.

VASP, the most popular one with much tutorials but commercial;

MS, has a Castep module with GUI, commerical or non-commerical;

QE, the most functional one, non-commerical;

GPAW, easily to write work-flow with atomic simulation enviroment, non-commerical

Pherhaps you can run your code on the super compute where you run LAMMPS. Or you can dump less data in LAMMPS.

Citra Hasanah sure, if you want to ask me, you can text me by email. This is my email ardiyantaruna8@gmail.com

Hello Rajiv Lakkaniga

Here are some basic understandings of meta-dynamics simulation

1. The collective variables determination is more important than Gaussian Height.

2. The higher Gaussian Height (H) will decrease simulation duration, i.e., decrease conformational sampling.

3. Decrease in H will increase simulation duration i.e., more detail about conformational sampling and space exploration.

4. The initial Gaussian height can (0.05kcal/mol), to decide the duration of the simulation to reach the equilibrium and after that frequency of the addition Gaussian (T_G) 0.09ps can be tuned as per your computational resources(power) and details want to explore.

5. The convergence can be judged based on free-energy calculations for each frame(g_mmpbsa)/free-energy surface to know about energy minima.

6. Conformational space/equilibrium exploration will be limited by the Wall (25 Å for distance) parameter, it can be tuned for more exploration.

Hi Tanvir,

There are several approaches to apply computational modelling and simulation to predict and investigate spin properties (e.g., SOC). I found MD based on LAMMPS or CASTEP are more reliable and, somehow, easy to implement. For your reference, I am listing below some journal articles explaining the procedure to follow (for illustration only, as I am sure that you will find more relevant to your research area):

1. LAMMPS: https://doi.org/10.1038/s41467-017-02260-2- Li-MinZheng work “Chiral expression from molecular to macroscopic level via pH modulation in terbium coordination polymers”

2. CASTEP: https://www.preprints.org/manuscript/202308.0076/v1- Zhang work, Preprint “ A Theoretical Analysis of the Differential Chemical Reaction Results Caused by Chirality Induction”

Good Luck Tanvir ur Rahman Chowdhury

Hi, could you please guide me how did you calculate the density profile in pore width?

You can use Google Cloud Platform or Amazon Web Services to perform MD simulations online. These platforms provide infrastructure and resources for scientific computing, including molecular dynamics simulations. You can set up your own computational environment and run simulations using software packages like GROMACS or AMBER. Additionally, you can use servers like Galaxy to perform simulations, which you can access by using the following link: https://usegalaxy-eu.github.io/index-cheminformatics.html

You could tell them that MD concerns itself with simulating how atoms and molecules move, while DFT concerns itself with the energy and properties that electrons determine for fixed atomic positions. Avoid terms like "dynamics", "functional" or "electronic structure". These might be too complicated for elementary school children. Use "motion", "energy" even "forces" instead.

You can get that information by running gmx hbond. For lifetime usually you use the Forward rate (just check the original publications on the tool).

Wenyi Ding Hey, are you still available at the same email ID? I am working with W-Cu alloy for my undergrad thesis, would be great if I could contact you.

For MD simulations in Gromacs, first enable WSL2 in your Windows

Here are some videos/links to help you with WSL2 setup -

Step 1: install Ubuntu 22.04 according to Microsoft's instructions

Step 2: refer starting from the 4 minute mark in this video: https://youtu.be/Rzg144v3hfo

Step 3: setting up a shared folder - you can access Windows drives by doing 'cd /mnt/c/' for C drive, or 'cd /mnt/d/' for D drive for example. You can also create a link to a desired folder. Refer video:

NVIDIA drivers for WSL2 : https://ubuntu.com/tutorials/enabling-gpu-acceleration-on-ubuntu-on-wsl2-with-the-nvidia-cuda-platform#2-install-the-appropriate-windows-vgpu-driver-for-wsl

Reboot WSL2 after installing NVIDIA drivers

Once you have WSL2 setup, install gromacs like you would on an Ubuntu machine - https://manual.gromacs.org/current/install-guide/index.html

To utilize GPUs while running your simulations on WSL2, or any machine with GPU, make sure this line is included in your MDP file: energygrps = System

Hi Julián Santiago Ruiz Castellanos,

In addition to Waseem Ahmad Ansari, molecular docking provides the initial prediction of the binding poses of a ligand against the target protein, also giving information on putative binding sites in the protein and significant residues involved in the ligand mode of action.

After this, one can select the best binding pose as input for molecular dynamics simulations for effective results.

Docking and simulations are complementary techniques, together providing a better understanding of the ligand-protein interactions.

First calculate distance between B-CD and drug then use your interested program like xmgrace, python and tcl

We have checked the RMSD, RMSF and Radius of gyration. There were no large scale conformational changes but still got spikes.

I had the same issues..... but interestingly cgenff server only support topologies for the following sulphur types..

### Supported S atoms in CGenFF

MASS  -1  SG2D1     32.06000 ! thiocarbonyl S MASS  -1  SG2R50    32.06000 ! THIP, thiophene MASS  -1  SG311     32.06000 ! sulphur, SH, -S- MASS  -1  SG301     32.06000 ! sulfur C-S-S-C type MASS  -1  SG302     32.06000 ! thiolate sulfur (-1) MASS  -1  SG3O1     32.06000 ! sulfate -1 sulfur MASS  -1  SG3O2     32.06000 ! neutral sulfone/sulfonamide sulfur MASS  -1  SG3O3     32.06000 ! neutral sulfoxide sulfur

Regards

Hi Daniel,

In addition to molecular dynamics, DFT can simulate the solvation dynamics of various polymers, including but not limited to DMSO, ETHANOL, METHANOL, and WATER. Examples of software cover Gaussian 09 and Biovia Material Studio. For molecular dynamics, you may use LAMMPS or BIOVIA Biovia Material Studio; please be advised that Material Studio software includes many modules that cover both quantum mechanics (e.g., DFT, HF). Quantum mechanics can predict potential and kinetic energies, but I am unsure about temperature, while molecular dynamics can provide them all.

Both approaches do have pros and cons, as well as challenges. Molecular dynamics can speed up the computations, but its accuracy is a function of many other parameters, such as the selection of the size of the unit cell representing the reaction and the full understanding of the reaction sequence and kinetics. Whereas simulation based on quantum mechanics is relatively slower, the reaction size can not exceed a hundred atoms at max – recall that molecular dynamics can have hundreds of thousands of atoms.

I did several computational modelling and simulation for ionic liquids and used both quantum mechanics and molecular dynamics to increase calculation repeatability and reproducibility. You can find in the literature many papers explaining the use of each, but I found a hybrid-based approach can predict results close to experimental results.