[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 gurbulako...@yahoo.com Date:

[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 ___

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

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] pdb2gmx error

On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul jalem...@vt.edu 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

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

Re: [gmx-users] pdb2gmx error

Ilya Chorny wrote: On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu 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

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

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

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

[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