Re: [gmx-users] Interpretation of MSD

Dear Akash, For local equilibration, your simulation time should be at least equal to Brownian relaxation time ~ a^2/D, where 'a' is particle radius and D is the 3D diffusion coefficient. This would imply that your MSD should be at least .6 * a^2. Some other possible checks: i. Make sure MSD

Re: [gmx-users] NVT.gro is not genetared

Thank you Nikhil. On Thu, Jun 29, 2017 at 9:47 AM, Nikhil Maroli wrote: > Hi, > see the log file for more information and correct the error, it is not > recommended to use -maxwarn without knowing the real problem. or share the > log file here. > -- > Gromacs Users mailing

[gmx-users] NVT.gro is not genetared

Dear gmx-users, I'm doing a CGMD simulation to a protein - DPPC system. After energy minimization, I used the following code to make a nvt.tpr and ran it. The nvt file was taken from the KELP_15 in DCCP in bevanlab tutorial. "gmx grompp -f nvt.mdp -c em_ions.gro -p elastic-w.top -n index.ndx

[gmx-users] tju....@gamil.com

tju@gamil.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

> > >> >> He he, childish :) > > David, no offense intended. I just think that when applied to solids, the entire concept of what works so well for biomolecular systems becomes a bit of a joke. And vice versa, to be fair. Spoken from experience, really -- we here used Gromacs to simulate things

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 186

Hi, Don't even consider running on more than one node. You can see for yourself by comparing the performance of even just e.g. gmx mdrun -nt 1 -pin on gmx mdrun -nt 2 -pin on gmx mdrun -nt 14 -pin on gmx mdrun -nt 28 -pin on ... to run on different numbers of cores. Parallel efficiency drops

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 186

Hi Mr. Abraham. My system is quite small, only about 8000 atoms. I have run this system for 100 ns, which took roughly about 2 days. Hence, a run of 1 microsecond would take about 20 days. I am trying to shorten it down to 2 days by using more than 1 node. Thanks, Thanh Le > On Jun 29, 2017, at

Re: [gmx-users] RemvingDummyAtoms

Hi, gmx trjconv can apply a selection (e.g. generated with gmx select) to your trajectory frames. gmx convert-tpr can do the same to your tpr, which you might need to help analysis work later on. Mark On Thu, Jun 29, 2017 at 10:57 PM Mostafa Javaheri < javaheri.grom...@gmail.com> wrote: > Dear

Re: [gmx-users] NoPbc

On Thu, Jun 29, 2017 at 7:29 PM Mostafa Javaheri wrote: > Dear gmx users > > I'm doing QM/MM simulation by using ORCA-Gromacs interface, the whole > simulation will take only 1 ps and I need to set pbc off. For this short > period of simulation does the pressure of

Re: [gmx-users] Running MD jobs using slurm on multiple nodes

Hi, Depends how many distinct simulations make sense to run. Normally you can make use of multiple simulations, so for a system of 20K+ atoms, efficiency is high if you run one simulation per node, compiled with thread-MPI, and leave mdrun to manage its own details. Otherwise, you could compile

[gmx-users] Running MD jobs using slurm on multiple nodes

Hi all, I am quite new to running MD jobs using slurm on multiple nodes. What confuses me is the creation of a slurm script. I don’t quite understand what inputs I should use to efficiently run. Please teach me how to create a slurm script and the md run command. Here are the info of the HPC:

[gmx-users] RemvingDummyAtoms

Dear gmx users I really appreciate it if anyone could tell me how could I remove dummy atoms from my trajectory? I made them before running the simulation for adding repulsive potential and now for analyzing the results there is no need for them. Regards M.Javaheri -- Gromacs Users mailing

Re: [gmx-users] Doubt about Free Energy control Minimization

Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more

Re: [gmx-users] Principale component analysis , experiment and MD comparison

On 6/29/17 2:32 PM, Nawel Mele wrote: Hi all, I would like to compare different MD trajectories with an ensemble of NMR structures by PCA. I performed the PCA by projecting all my MD structures and NMR ensemble onto the eigenvectors of my NMR ensemble then plot the result. This method is

[gmx-users] Principale component analysis , experiment and MD comparison

Hi all, I would like to compare different MD trajectories with an ensemble of NMR structures by PCA. I performed the PCA by projecting all my MD structures and NMR ensemble onto the eigenvectors of my NMR ensemble then plot the result. However, I also performed PCA for each MD trajectories

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

On 28/06/17 20:22, Alex wrote: This community is mostly focused on other things. If you have solid silica under a non-native (to Gromacs) forcefield and all the bonded parameters have been copied correctly, there may be issues with your partial charges, LJ parameters, and mixing rules. Also make

Re: [gmx-users] In-vacuo minimization of peptide

On 6/29/17 8:29 AM, Apramita Chand wrote: Dear All, I have constructed the initial structure of peptide using Pymol and energy-minimizing it using steepest-descent algorithm(both with and without restraints) with the conditions: integrator = steep ; Algorithm (steep = steepest descent

[gmx-users] NoPbc

Dear gmx users I'm doing QM/MM simulation by using ORCA-Gromacs interface, the whole simulation will take only 1 ps and I need to set pbc off. For this short period of simulation does the pressure of the box change? Does the water vaporize after 500 steps? Any helps will be appreciated. Regards

[gmx-users] Interpretation of MSD

Hi all, I performed Mean Square Deviation for my ligand molecules in x, y, z directions in order to obtain the diffusion coefficients. From my understanding, the square root of the highest MSD value should be significant enough to interpret that the ligand molecules have in fact moved enough

[gmx-users] In-vacuo minimization of peptide

Dear All, I have constructed the initial structure of peptide using Pymol and energy-minimizing it using steepest-descent algorithm(both with and without restraints) with the conditions: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when

Re: [gmx-users] Invalid angle type 0

On 6/29/17 6:52 AM, Zuzana Benkova wrote: Dear GROMACS users, I have prepared a topology file for a carbon nanotube according to the GROMACS tutorial. I have also checked the generation of bonds, angles and dihedrals and visualized the gro file before. Everything looks correctly. However,

Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I am getting the same following warning even after minimizing the system twice using cg integrator. This is only when the free energy stuff is inserted in the energy minimization code. " WARNING: Listed nonbonded

[gmx-users] Invalid angle type 0

Dear GROMACS users, I have prepared a topology file for a carbon nanotube according to the GROMACS tutorial. I have also checked the generation of bonds, angles and dihedrals and visualized the gro file before. Everything looks correctly. However, when I wanted to prepare the tpr file for the

Re: [gmx-users] Doubt about Free Energy control Minimization

Dear Justin, I am getting the same following warning even after minimizing the system twice using cg integrator. This is only when the free energy stuff is inserted in the energy minimization code. " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at distance 3f which is

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 181

Hi, Thanks Alex. I have now solved the problem. I assumed ³gen - pairs = yes² within [ Defaults ] of the topology was generating automatically a list of pairs of 1-4 interactions as well as modifying the LJ and QQ parameters for those interactions. I have now listed the 1-4 pairs within [ Pairs

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

Hi Sudip, we had a short discussion over coffee. We also get these warnings, but they don't generally lead to significant instabilities. This means you probably have an equilibration issue. Could you try equilibrating your system with increasing timesteps? So first equilibrate with 5fs, then

Re: [gmx-users] NPT error

Hi, I tried -dd option with (7 2 1) value and got this error: Fatal error: 1130 particles communicated to PME rank 14 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

Hi Sudip, there's a dedicated forum for these Martini questions on cgmartini.nl. Recently there was a similar question there (http://cgmartini.nl/index.php/component/kunena/7-mdp-options/5491-gpu-verlet-oscillational-period#7308). To summarize, the bonds between the backbone beads are extremely

[gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

Dear All, I am running a CGMD simulation of protein and surfactant in water with Martini2.0 force field for surfactant and water and ELNEDYN2.2 force field for protein. The system is running fine with 20 fs integration timestep. But it leads to solid phase of water. So, I have introduce