[gmx-users] Gromacs 5.0 Benchmarking Systems

Good Morning, I am a graduate student at the University of Colorado at Boulder. The University is in the process of transitioning to a new supercomputer and the Research Computing team who is in charge of setting it up said that they would be happy to benchmark Gromacs on the computer if I

[gmx-users] cgenff CTAB

Dear all, I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 force field in GROMACS. However, it always gives the wrong error message, saying that the number of atoms does not match the .top. I wonder what could be the reason for this problem. Attached are .mol2 and .str

Re: [gmx-users] cgenff CTAB

On 3/29/16 5:40 PM, xy21hb wrote: Dear all, I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 force field in GROMACS. However, it always gives the wrong error message, saying that the number of atoms does not match the .top. I wonder what could be the reason for this

[gmx-users] Generate diagram/figure with information about protein-ligand interactions

Hi, after a protein-ligand simulation with gromacs, I would like to be able to generate a diagram/figure with information about protein-ligand interactions, something like this: https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg

Re: [gmx-users] cgenff CTAB

https://www.dropbox.com/s/bptog3lgtyp9qt2/CTAB.zip?dl=0 Dear Justin, Above is the link to the mol2 and str files. I checked the naming of the input files and the same error remained. Thanks, Yao At 2016-03-30 05:42:25, "Justin Lemkul" wrote: > > >On 3/29/16 5:40 PM,

Re: [gmx-users] cgenff CTAB

On 3/29/16 6:32 PM, xy21hb wrote: https://www.dropbox.com/s/bptog3lgtyp9qt2/CTAB.zip?dl=0 Dear Justin, Above is the link to the mol2 and str files. I checked the naming of the input files and the same error remained. It's exactly as I expected; in the stream file you have: RESI /scrat

Re: [gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method

On 3/28/16 9:02 PM, Khuong Truong Gia wrote: Dear all, I am running umbrella sampling simulation about binding of a drug (polymer) to a lipid bilayer. Could you please suggest me how can I do position-restraints the reference group (bilayer)? Do I need to restraint all lipid molecules? You

Re: [gmx-users] Query on g_mmpbsa in gromacs

On 3/29/16 1:25 AM, Prasanna Dr wrote: Hi, Thanks for your quick response. AMBER mmpbsa does amino-acid pairwise residue decomposition. Pairwise decomposition energy is very suitable input for weighted network analysis (to understand the information flow between residues and to find key

Re: [gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method

Dear Justin, I got it. Thank you very much for your kindly reply. Best regards, Khuong On Tue, Mar 29, 2016 at 6:56 PM, Justin Lemkul wrote: > > > On 3/28/16 9:02 PM, Khuong Truong Gia wrote: > >> Dear all, >> >> I am running umbrella sampling simulation about binding of a

[gmx-users] maxh mdrun option does not work with REMD simulation

Dear Gromacs users, I tried to do a REMD simulation with gromacs 5.1 which is re-launched every hour (in a queuing system) with the -maxh option. The first time it was launched, it worked : the run stoped at the maxh time and it was re-launched with the checkpoint files and continued the

Re: [gmx-users] Query on g_mmpbsa in gromacs

Pairwise interaction scheme ​ is not implemented in g_mmpbsa. Therefore, g_mmpbsa cannot be used to calculate interaction energy between two residues. With best regards, ​Rajendra ​ On Mon, Mar 28, 2016 at 2:37 PM, Prasanna Dr wrote: > Hi > > I have been using

[gmx-users] Turn-off the long range Van der Waals interactions

Dear Gromacs users, May I know, how to turn-off the long range Van der Waals interactions during simulations ? Thanks Krishna Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us

[gmx-users] Turn-off the long range Van der Waals interactions

Dear Gromacs users, May I know, how to turn-off the long range Van der Waals interactions during simulations ? Thanks Krishna Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify

Re: [gmx-users] Turn-off the long range Van der Waals interactions

Hi Mark, Actually, I want to exclude long range interaction potentials (both coulombic and LJ) of some of the molecules. Thanks Krishna -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of

Re: [gmx-users] on the gromacs force field for keep helix

Hi Brett, There is no GROMACS force field. Now the original GROMOS force fields 53a5 and 53a6 are known to be more unstable in the helix department than they should, so better not use those. There are newer versions of 53a6 and there's 54a7, which are fine. I'm actually not entirely sure what

Re: [gmx-users] Turn-off the long range Van der Waals interactions

Hi, What do you mean by "long-range Van der Waals interactions?" Mark On Wed, Mar 30, 2016 at 4:07 AM Krishna Mohan Gupta wrote: > Dear Gromacs users, > > May I know, how to turn-off the long range Van der Waals interactions > during simulations ? > > Thanks > Krishna > > >

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

I have not looked at your link yet but I believe PyMol is best for generating high quality figures. You can explore a number of options in pymol. Regards Suniba Sent from my iPhone > On 30-Mar-2016, at 3:15 am, bio hpc wrote: > > Hi, > > after a protein-ligand

Re: [gmx-users] Flat-bottom potential SEGFAULT

> On 28 Mar 2016, at 01:52, Justin Lemkul wrote: > > > > On 3/26/16 12:47 PM, Erik Marklund wrote: >> Dear dynamicists, >> >> I am using flat bottom potentials to prevent water molecules from >> evaporating from a droplet in vacuum. The manual suggests this is pretty >>

[gmx-users] on the gromacs force field for keep helix

Dear All, Before I read some on-line material , perhaps the on-line tutorial of Justin. It said there was a gromacs force field better than the other gromacs force field for keeping the intact of the helix during MD. WIll you please tell me which is the force field used for keeping the intact

[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

Dear Users: I am trying to do some Hamiltonian replica exchange (H-REMD) in gromacs 5.1.2 and am running up against really large slowdowns when decoupling a large number of atoms. I am decoupling 5360 atoms out of the 15520 atoms in my system. The goal is not to get a PMF, but to enhance