Re: [gmx-users] GPU calculation of GROMACS in Windows System

li ming wrote: Hi! all: I am informed in OPENMM website that the OPENMM can accelerate GPU calculation of GROMACS in Windows System. How can I apply this method to my study? Any ideas will be welcomed!!! Probably you can't incorporate it in any conventional MD study. See the supported fea

[gmx-users] GPU calculation of GROMACS in Windows System

Hi! all: I am informed in OPENMM website that the OPENMM can accelerate GPU calculation of GROMACS in Windows System. How can I apply this method to my study? Any ideas will be welcomed!!! My display card in my PC is in ATI series, and the lib of OPENMM is not provided in OPENMM website...So I g

Re: [gmx-users] pdb2gmx error

Thanks, this very helpful!!! Sent from my iPhone On Mar 15, 2009, at 3:48 PM, "Justin A. Lemkul" wrote: Tsjerk Wassenaar wrote: Hi, --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87 Fatal er

Re: [gmx-users] pdb2gmx error

Tsjerk Wassenaar wrote: Hi, --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1094904186 while adding improper ---

Re: [gmx-users] pdb2gmx error

Hi, >>        --- >>        Program pdb2gmx, VERSION 4.0.3 >>        Source code file: pgutil.c, line: 87 >> >>        Fatal error: >>        Atom N not found in residue 1094904186 while adding improper >> >>        --

Re: [gmx-users] pdb2gmx error

Ilya Chorny wrote: On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul > wrote: Ilya Chorny wrote: I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new re

Re: [gmx-users] about MARTINI forcefield

The first ting to do would be to read the later papers describing the philosophy of the force field. There you'll find clear examples of how small molecules can be parameterized. This goes in two main steps: i) geometrization: define the number of beads, bonds, angles, dihedrals to descri

Re: [gmx-users] pdb2gmx error

On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul wrote: > > > Ilya Chorny wrote: > >> I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached >> to the side chain nitrogen called ASBG. I want to test the new residue by >> itself. >> >> When I pdb2gmx it I get the following erro

Re: [gmx-users] How can I record only molecule trajectory ?

Chih-Ying Lin wrote: Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? Use xtc_grps in the .mdp file, or use

Re: [gmx-users] How can I record only molecule trajectory ?

Chih-Ying Lin wrote: Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? If you mean protein only then check either

[gmx-users] How can I record only molecule trajectory ?

Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? Thank you Lin ___ gm

[gmx-users] Fwd: using oplsaa in Gromacs

I refuse to act as a mailing-list subsitute. And there are others better fit to point you to: http://www.catb.org/~esr/faqs/smart-questions.html http://wiki.gromacs.org/index.php/Parameterization Tsjerk -- Forwarded message -- From: oguz gurbulak Date: Sun, Mar 15, 2009 at 2:50