Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7

Hi, On Fri, Sep 18, 2015 at 6:27 AM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > > I have a system with many distance restraints, designed to maintain > helical character, e.g.: > [ distance_restraints ] > 90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0 > 97 57 1 2 2 2.8

[gmx-users] Custom elastic network of a membrane protein

Hi all, I am simulating a membrane protein in DPPC in order to insert it in the bilayer. I did a previous run during 2 us and I saw major changes in the secondary structure. Now I want to use an elastic network in order to preserve the overall secondary structure. It is possible to build an

[gmx-users] Running two separate mdrun instances on a single workstation

Hello gmx users, I have a two-socket (8 physical cores each, and with hyperthreading 32 cores system) with 2 gpus. I want to run two independent simulations using 16 threads and a single GPU. I tried the -pin on and -pinoffset 0 for the first instance of mdrun and -pin on and -pinoffset 8 for th

Re: [gmx-users] Running two separate mdrun instances on a single workstation

Hi, pinoffset 0 and 16 should be correct, these should place threads on what's shown as "CPU" idx 1-8,17-24 and 9-16,25-32, resp. Cheers, -- Szilárd On Fri, Sep 18, 2015 at 11:59 AM, Deva Priya wrote: > Hello gmx users, > > I have a two-socket (8 physical cores each, and with hyperthreading 3

Re: [gmx-users] New atom definition

On 9/18/15 12:20 AM, Maryam Kowsar wrote: Thaks justin! I did it several times and it worked. But now when i want to add some neutral gas or heavy atoms it stops me with the error that the atom is not defined. I dont know where i make a mistake. Neither does anyone here, because you haven't

Re: [gmx-users] Electric double layer, how to add charge

Hi Andreas, I use OPLSAA myself, and although it gets the wrong figures for the surface potential and other interfacial properties, it is a known bias and you know in which direction your results are going wrong. IMHO, switching to other non-polarizable forcefield wouldn't work either, since most

[gmx-users] (no subject)

Hello, How can I restrain the position of one group of molecules, but let them interact with other molecules free to move within the system? Thanks, Anand Dharia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before post

[gmx-users] Clustering of Molecules Gromacs

Hello, I am wondering if there is any built-in method that Gromacs may have to quantify the extent of clustering between protein molecules. Thanks, Anand Dharia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

Re: [gmx-users] (no subject)

On 9/18/15 7:30 PM, ANAND AMITKUMAR Dharia wrote: Hello, How can I restrain the position of one group of molecules, but let them interact with other molecules free to move within the system? Position restraints do not affect nonbonded interactions. -Justin -- =

Re: [gmx-users] Clustering of Molecules Gromacs

On 9/18/15 7:46 PM, ANAND AMITKUMAR Dharia wrote: Hello, I am wondering if there is any built-in method that Gromacs may have to quantify the extent of clustering between protein molecules. There are plenty of things you can calculate. Consult Chapter 8 of the manual. gmx cluster, gmx cl

Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7

Dear Mark: you are correct. If I get rid of the gmx_fatal call then everything seems to work just fine. In the file src/gmxlib/disre.c , I got rid of the following code, which starts on line 147 of gmx 4.6.7: if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||