[gmx-users] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz

Sorry, abrupt sending, the coulombtype is the same coulombtype = cut-off and constraints = all-bonds is the same. Any idea? 2011/1/27 Camilo Andrés Jimenez Cruz > Hi all! > > I am trying to run the dppc example located in > ftp://ftp.gromacs.org/pub/benchmarks/

[gmx-users] Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz

Hi all! I am trying to run the dppc example located in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz, with the gpu version of gromacs, when I run it I get WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. ---

[gmx-users] trjconv -fit rot+trans before a pbc? safe way to rotate a trajectory?

Hi list! it has been discussed in other posts the inconvenience of PBCing after rotating (see example: http://oldwww.gromacs.org/pipermail/gmx-developers/2009-November/003754.html), I just want to know what is the state of this problem and if somebody has found a satisfying solution. I also wonde

Re: [gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

Thanks, I found the problem, I was using a wrong index file :P My bad, On Wed, Apr 7, 2010 at 8:32 PM, Mark Abraham wrote: > On 8/04/2010 10:22 AM, Camilo Andrés Jimenez Cruz wrote: > >> Hi all >> >> I am using gromacs-3.3.99's g_sas_s in a long trajectory and I

[gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

Hi all I am using gromacs-3.3.99's g_sas_s in a long trajectory and I get this error right away. I assume its memory capacity, is there a way (other than cutting the trj in smaller chunks?) Select a group: Select a group: *** glibc detected *** /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s: mal

Re: [gmx-users] How to change the protonation state of an aminoacid in a peptide

A. Lemkul wrote: > > > Camilo Andrés Jimenez Cruz wrote: >> >> Hi. >> >> I have the gro file for a peptide in vacuum, in the peptide, there is >> only one ASP, and I want to change it to ASPH. >> If I run pdb2gmx -asp and select the protonated stat

[gmx-users] How to change the protonation state of an aminoacid in a peptide

Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing th

[gmx-users] How to cap a peptide using pdb2gmx

Hi everybody I downloaded a pdb entry from RCSB and it comes with charged terminii, for example, the first aminoacid is ATOM  1  N   ASN A   1  -8.901   4.127  -0.555  1.00  0.00   N ATOM  2  CA  ASN A   1  -8.608   3.135  -1.618  1.00  0.00   C ATOM  3  C   A