[gmx-users] Barostat relaxation times

UNRESTRICTED / ILLIMITÉE Dear Gromacs users, Does anyone have any advice on how to choose an appropriate barostat relaxation time? I'm quite new to molecular dynamics, and I am running some simple simulations of a box of water using a Nose-Hoover thermostat, a Parrinello-Rahman

Re: [gmx-users] about CHARMM force field in GROMACS

On 9/22/16 1:56 PM, jing liang wrote: Hi, in GROMACS web site there is a recommendation when using CHARMM27 set of parameters: constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME rcoulomb = 1.2

[gmx-users] about CHARMM force field in GROMACS

Hi, in GROMACS web site there is a recommendation when using CHARMM27 set of parameters: constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME rcoulomb = 1.2 DispCorr = no Is there some issue with the

Re: [gmx-users] Running Gromacs in parallel

Thanks again > On Wed, Sep 21, 2016 at 9:55 PM, wrote: >> Thanks Sz. >> >> Do you think going up to from version 5.0.4 to 5.1.4 would really make >> such a big difference? > > Note that I was recommending using a modern compiler + the latest > release (which is

[gmx-users] Chloroform Density problem

Dear Users, I am trying to solvate small organic molecule (8 molecules) of 20 atoms each =160 atoms in Chloroform using Genbox. according to the box volume that is created by the editconf (truncated octahedron of 6nm) that is 166.28 nm, it should have roughly 1200 molecules of chloroform. (not

Re: [gmx-users] Running Gromacs in parallel

On Wed, Sep 21, 2016 at 9:55 PM, wrote: > Thanks Sz. > > Do you think going up to from version 5.0.4 to 5.1.4 would really make > such a big difference? Note that I was recommending using a modern compiler + the latest release (which is called 2016 not 5.1.4!). It's

[gmx-users] xpm2ps

Dear all, I have generated *.xpm file using dssp and trying to convert it into eps i used gmx xpm2ps -f dssp.xpm -o abc.eps -do new.m2p -di new.m2p and my new.m2p file is given as https://drive.google.com/file/d/0BxaQk_pcR9viRWtVdlhRdU90SlU/view? usp=sharing When i visualize the eps file using

Re: [gmx-users] car_to_files.py in AMBER16 is not available.

On 9/22/16 4:49 AM, Jinfeng Huang wrote: Dear gromacs users, I follow the tutotial of "Setting Up A Hydroxyaptite Slab in Water Box" (http://ambermd.org/tutorials/advanced/tutorial27/hap_water.htm) and met a problem. The pyMSMT package in Amber16 does not have car_to_files.py procedure

Re: [gmx-users] gmx sans crashes or return nan's

How big is the system? This happened to me when my system required too much memory to finish the computation. You could try running it on a subset for your whole system to see if it works or just run it on a subgroup (not on the group "System") to confirm if this is the problem. Another thing to

Re: [gmx-users] Free Energy of Binding Question

On Wed, 21 Sep 2016 12:00:29 + Abdülkadir KOÇAK wrote: > In terms of endstates, the state A is the real ligand complexed with > Protein in water... I did not define dummy atoms for the ligand as > the state B, which I believe I should have... I'm not quite sure what you

[gmx-users] car_to_files.py in AMBER16 is not available.

Dear gromacs users, I follow the tutotial of "Setting Up A Hydroxyaptite Slab in Water Box" (http://ambermd.org/tutorials/advanced/tutorial27/hap_water.htm) and met a problem. The pyMSMT package in Amber16 does not have car_to_files.py procedure and so as the pyMSMT package in

[gmx-users] gmx sans crashes or return nan's

Hi, I've tried to run gmx sans tool on our trajectory but unfortunately it crashes or returns -nan. The crash is when it is compiled in Release mode. I have used the latest 2016 release. GROMACS: gmx sans, version 2016 gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10 Select a

Re: [gmx-users] g_membed failure

Thank you so much Tom, I will try that! 2016-09-21 21:11 GMT+03:00 Thomas Piggot : > g_membed is now part of mdrun, so you would need to use mdrun with the > -membed option. From mdrun -h: > > /"The option -membed does what used to be g_membed, i.e. embed a protein > into

Re: [gmx-users] Interest of c alpha atoms for least square fitting?

Yes > On 22 Sep 2016, at 06:45, Seera Suryanarayana wrote: > > Dear gromacs users, > > Can I give my interest of c alpha atoms for least square fitting in gmx rms > for RMSD calculation? > > Thanks in advance > Surya > Graduate student > India. > -- > Gromacs Users