[gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out

Dear Gromacs Community, I have come across this problem during NVT equilibration of an all atom protein-ligand MD simulation. Fatal error: 1 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

[gmx-users] distance from geometrical center of protein to the surface

Hello everyone, I have run simulation of protein interacting with the infinite slab of polymer surface and now I'm trying to calculate the distance between protein geometrical center and the closest atom of the surface. I have read through the manual but still don't understand how to measure such

[gmx-users] gmx rms divergence from the starting structure

Hello everyone, I am trying to evaluate the convergence of protein structure during simulation to equilibrium state with "gmx rms", however I see strange (to me) results when RMSD goes from high in the beginning of simulation to low in the end of simulation - I would expect the trend to be

[gmx-users] PCA analysis with different atoms in -s and -f

I am trying to compare trajectories from different MD simulations, including different pH and different mutants. The initial PDB (i.e. 0.pdb) is the same, but the derived PDBs (1.pdb, 2.pdb, etc.) are different due to protonation states and mutations. Those different PDBs were used individually

Re: [gmx-users] Effect of atomic charge on bonding parameters

On 3/31/20 8:05 PM, Neena Susan Eappen wrote: Hello gromacs users, Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible? ; name

Re: [gmx-users] 1-4 LJ interactions

On 3/31/20 12:59 PM, Andrey Gurtovenko wrote: Dear All, Recently I realized that I don't fully understand what should be done in Gromacs to account for 1-4 LJ interactions. According to the manual: "gen-pairs is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the

Re: [gmx-users] How to reduce the penalty of small molecule from CGenFF

On 3/29/20 1:29 AM, Rolly Ng wrote: Hello Justin, Thank you and yes. I went to the paper and it shows the steps for optimization. However, I have the following problems as I tried to follow the tutorial on CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor (1) what

Re: [gmx-users] Different force constants for different umbrella windows?

On 3/31/20 2:07 AM, Andreas Mecklenfeld wrote: Dear GROMACS users, I've a question regarding umbrella sampling and its evaluation with gmx wham. Is it possible to use different force constants for different umbrella windows? Yes. -Justin --

[gmx-users] Effect of atomic charge on bonding parameters

Hello gromacs users, Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible? ; name bond_type masscharge ptype

[gmx-users] 1-4 LJ interactions

Dear All, Recently I realized that I don't fully understand what should be done in Gromacs to account for 1-4 LJ interactions. According to the manual: "gen-pairs is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the

Re: [gmx-users] Onsager coefficient

Thanks, recently there have been studies that found a good match between MD simulations and experimental results for multicomponent systems and shows that there is a good chance for finding a relation for diffusion coefficient as a function of concentration. Self-diffusion coefficients can be used

Re: [gmx-users] Onsager coefficient

Den 2020-03-31 kl. 16:01, skrev Sina Omrani: it is Maxwell-Stefan. I want to calculate diffusion coefficients. from EMD we can calculate the MS diffusion coefficient that it is impossible to measure experimentally (because it is based on chemical potential gradient that is hard to measure)

Re: [gmx-users] Onsager coefficient

it is Maxwell-Stefan. I want to calculate diffusion coefficients. from EMD we can calculate the MS diffusion coefficient that it is impossible to measure experimentally (because it is based on chemical potential gradient that is hard to measure) and with the thermodynamic correction factor it

Re: [gmx-users] Onsager coefficient

Den 2020-03-31 kl. 14:11, skrev Sina Omrani: As far as I know, the Onsager coefficient is used to calculate MS diffusion coefficient that is a microscopic property. Then we can use this MS coefficient and relate it to macroscopic properties that we already have experimentally. What does MS

Re: [gmx-users] Onsager coefficient

As far as I know, the Onsager coefficient is used to calculate MS diffusion coefficient that is a microscopic property. Then we can use this MS coefficient and relate it to macroscopic properties that we already have experimentally. On Tue, 31 Mar 2020 at 11:05, David van der Spoel wrote: > Den

Re: [gmx-users] replica exchange simulations performance issues.

On Tue, Mar 31, 2020 at 1:45 AM Miro Astore wrote: > I got up to 25-26 ns/day with my 4 replica system (same logic scaled > up to 73 replicas) which I think is reasonable. Could I do better? > Hard to say without complete log file. Please share single run and multi run log files. > > mpirun

Re: [gmx-users] Extracting information from trajectory

Hi, I want to run numerous equilibrations of pure systems (i.e. numerous identical molecules in a box) and then extract multiple measurements (multiple bond angles, bond lengths, dihedrals etc.), and I will need to do this for all the molecules in the system once equilibrium is reached. Any

[gmx-users] itp file for TIP7P

Dear all, I've seen the recent publication about the tip7p model (https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out in some simple MD simulations. Since I am still a pretty new Gromacs user, I didn't want to build the itp file myself and, potentially or most probably,

[gmx-users] Different force constants for different umbrella windows?

Dear GROMACS users, I've a question regarding umbrella sampling and its evaluation with gmx wham. Is it possible to use different force constants for different umbrella windows? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik

Re: [gmx-users] Onsager coefficient

Den 2020-03-31 kl. 08:17, skrev Dallas Warren: 3.5.9 Onsager Relations https://www.iue.tuwien.ac.at/phd/mwagner/node44.html See 3.146 and 3.147 Thanks, I admit I am not familiar with this stuff, but seeing that this falls under the heading "Macroscopic Transport Models", what is the point

Re: [gmx-users] Onsager coefficient

3.5.9 Onsager Relations https://www.iue.tuwien.ac.at/phd/mwagner/node44.html See 3.146 and 3.147 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu