[gmx-users] problem with dihedral restraints in gromacs 5.1.4.

Hello, I have tried to introduce dihedral restraints in gromacs 5.1.4. I modified topology file and mdp file as following:   In my topology file, #ifdef DIHRE [ dihedral_restraints ] ; ai  aj  ak  al   type   phi   dphi   kfac    7   8  9   10 1  180   0  100    7   8  9   14 1 

Re: [gmx-users] performance

Hi Szilárd, Sorry this discussion is going long. Finally I got one node empty and did some serious tests specially considering your first point (discrepancies in benchmarking comparing jobs running on empty node vs occupied node). I tested in both ways. I ran following cases (single job vs two

[gmx-users] md simulation for magnetic nanomaterials

Dear Sir I know gromacs do some md simulation for biological system. I want to do some md simulation on magnetic nanomaterials. Can you anyone give me some idea which software do md simulation for magnetic nanomaterials. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of

Re: [gmx-users] Coordinates not matching with topology file

Hello, You can look into which files you have downloaded from the ATB server. Since gromos53a6 is the ff employed, ATB will generate both all atom (AA) and united atom (UA) models. Make sure you have taken the correct (say) UA coordinate and the corresponding UA itp (topology) files. Make sure

[gmx-users] Ionic liquid simulation problem

> Dear GROMACS Community, > > I am very new with GROMACS I am trying to run a simulation of an ionic liquid > (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the > following protocol: > > 1. Prepared the respective PDB files and added/modified the OPLS/AA force > field

[gmx-users] PMF calculation: molecule though the channel.

Dear all, Im trying to pull water molecules through Aquaporin channel with the following pull parameters (to obtain PMF). On visualising the trajectory, water molecules travelling around the surface/outside of aquaporin instead of going through inside. How I can make sure that the water molecule

Re: [gmx-users] .XTC file could not be found after simulation completion

Okay ;) nstxout-compressed = XXX ; write .xtc trajectory every /Y ps -- 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

Re: [gmx-users] .XTC file could not be found after simulation completion

Hi, Nitpick: the "nst" is "number of steps" so setting it to X doesn't necessarily give you a frame every X picoseconds ;-) Mark On Thu, 14 Sep 2017 06:45 Nikhil Maroli wrote: > Yes, sorry mistake. > > nstxout-compressed = XXX ; write .xtc trajectory every XXX ps >

Re: [gmx-users] performance

Hi Szilárd, Here are my replies: >> Did you run the "fast" single job on an otherwise empty node? That might explain it as, when most of the CPU cores are left empty, modern CPUs increase clocks (tubo boost) on the used cores higher than they could with all cores busy. Yes the "fast" single job

Re: [gmx-users] performance

On Wed, Sep 13, 2017 at 11:14 PM, gromacs query wrote: > Hi Szilárd, > > Thanks again. I tried now with -multidir like this: > > mpirun -np 16 gmx_mpi mdrun -s test -ntomp 2 -maxh 0.1 -multidir t1 t2 t3 t4 > > So this runs 4 jobs on same node so for each job np is = 16/4,

[gmx-users] Coordinates not matching with topology file

We have generated the *.gro and *.itp file from the ATB server and then did editconf and solvate. The error that's coming is: Fatal error: number of coordinates in coordinate file (g12wt.gro, 33766) does not match topology (g12.top, 33698) If you notice, the error is of 68 atoms.