[gmx-users] problem with force fields while running membrane protein simulation

2011-02-04 Thread Mohana lakshmi
Dear all and Justin... I am trying to do membrane protein simulation by following justin's tutorial using gromacs 4.5.3 version. I selected ffG53a6 force field and pasted the content of lipid.itp file to the corresponding files as per the instructions in the tutorial but i got error (Fatal error:

Re: [gmx-users] problem with force fields while running membrane protein simulation

2011-02-04 Thread Mark Abraham
On 4/02/2011 7:54 PM, Mohana lakshmi wrote: Dear all and Justin... I am trying to do membrane protein simulation by following justin's tutorial using gromacs 4.5.3 version. I selected ffG53a6 force field and pasted the content of lipid.itp file to the corresponding files as per the instructi

Re: [gmx-users] problem with force fields while running membrane protein simulation

2011-02-04 Thread Mohana lakshmi
Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. -- Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] problem with force fields while running membrane protein simulation

2011-02-04 Thread Mark Abraham
On 4/02/2011 9:00 PM, Mohana lakshmi wrote: Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. Please leave the context for the discussion in subsequent emails. You ca

Re: [gmx-users] problem with force fields while running membrane protein simulation

2011-02-04 Thread Mohana lakshmi
Thank you Mark. Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use

[gmx-users] what standard is successful when doing EM

2011-02-04 Thread gromacs
Hi, guys Water molecule starting at atom 10578 can not be settled. Check for bad contacts and/or reduce the timestep. When i run 6x6x1.3nm water box. i used several methods to do EM. So i can do several EM. But which .gro should i select as my input .gro for my running？ Because when i use diffe

Re: [gmx-users] what standard is successful when doing EM

2011-02-04 Thread Mark Abraham
On 4/02/2011 10:07 PM, gromacs wrote: Hi, guys Water molecule starting at atom 10578 can not be settled. Check for bad contacts and/or reduce the timestep. When i run 6x6x1.3nm water box. i used several methods to do EM. So i can do several EM. But which .gro should i select as my input .gro f

Re: [gmx-users] problem with force fields while running membrane protein simulation

2011-02-04 Thread Justin A. Lemkul
Mark Abraham wrote: On 4/02/2011 9:00 PM, Mohana lakshmi wrote: Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. The tutorial is not compatible with version 3.3.

[gmx-users] Re: Energy calculation problem with molecule leaving the box

2011-02-04 Thread Gordan Horvat
I extracted trajectories with -pbc center -mol to obtain ones with molecules that form different energy groups in all combinations and then rerunned the simulation. This procedure was described here http://lists.gromacs.org/pipermail/gmx-users/2007-October/030104.html I seem to get a reasonable

[gmx-users] Error Messages

2011-02-04 Thread simon sham
Hi, I  run GROMACS in parallel mode. The first two jobs that I submitted are still running. However, when I tried to submit the third job, and stopped for the following reason: Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell siz

Re: [gmx-users] Error Messages

2011-02-04 Thread Justin A. Lemkul
simon sham wrote: Hi, I run GROMACS in parallel mode. The first two jobs that I submitted are still running. However, when I tried to submit the third job, and stopped for the following reason: Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box

[gmx-users] harmonic restraint with OpenMM

2011-02-04 Thread Jochen Hub
Hi, I am trying to restrain an ion that is coordinated by a few protein atoms, to avoid that the ion might fly off. The simulation should be run on a GPU (with OpenMM) and implicit solvent. First I tried to restrain the ion using bonds of type 6, but harmonic potentials are not supported by O