[gmx-users] Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0?

Dear Gmx users, I want to simulate a protein which has phosphorelated residues. Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0 or 4.6? I have got following error: Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pgutil.c, line: 126 Fatal error: Residue

[gmx-users] Segmentation fault error

*Dear all,* *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL in the form of a vesicle. The code works well for the system when the CHOL molecules are not inserted. As I include CHOL molecules I face this error:* *starting mdrun 'Chol/HSPC VESICLE'90

[gmx-users] Maximun time-step recommended in the grompp part for each system

Dear all, Taking look at the check_bonds_timestep() function in src/kernel/grompp.c used for checking the time-step used for the integration of the equations of motion a few questions come to me: - In the comments of the function it is said that The stability limit of leap-frog or velocity

Re: [gmx-users] Morse potential for Specific Group

On Dec 10, 2014 10:21 PM, Jackson Chief Elk jchief...@gmail.com wrote: Hi, I am building my own routine to use the Gromacs API to do MS-EVB. I need to treat O-H bonds of 1 hydronium ion with a Morse Potential. How can I specify in the *.mdp file, to just describe bonding in hydronium using

[gmx-users] xeon-phi and double precision

Hi. Does xeon-phi make double precision gromacs faster? -- 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 (un)subscribe requests visit

[gmx-users] Segmentation fault error

*Dear all,* *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL in the form of a vesicle. The code works well for the system when the CHOL molecules are not inserted. As I include CHOL molecules I face this error:* *starting mdrun 'Chol/HSPC VESICLE'90

Re: [gmx-users] Segmentation fault error

Hi, This is a generic MPI error message. Nobody can tell from it what caused it. You need to look at the whole stdout and the mdrun .log file for diagnostics. You should also report your Gromacs version. Probably you are just http://www.gromacs.org/Documentation/Terminology/Blowing_Up, but there

Re: [gmx-users] xeon-phi and double precision

Hi, Probably not by much. Your best bet is to talk someone else into running on it, so that you can run mdrun on the resources they'd otherwise consume. :-) Mark On Fri, Dec 12, 2014 at 3:34 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Does xeon-phi make double precision gromacs faster?