[gmx-users] General Questions abdout gromacs

Sven Huttenhouse mdsimulation at hotmail.com
Mon Nov 21 18:11:24 CET 2005

Thank you all for replying

What is the command that I have to use to run the mdrun in the backgroun?
where can I learn (read more) about  LINCS or SHAKE??

kind regards

>From: Marcus Kubitzki <mkubitz at gwdg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] General Questions abdout gromacs
>Date: Fri, 18 Nov 2005 10:50:13 +0100
>>2- I'm running a simulation for 64 glycine molecules with 449 water 
>>molecules. I need to run this for the first one second but the time step 
>>in the .mdp file is 1fs and the program doesn't work if I increase the 
>>time step. is there any other way I can speed up the simulation?
>Simulating your system for one second(!) requires a little bit of patience. 
>Depending on hardware, ffield & water model a system of ~2000 atoms (my 
>estimate) evolves a few ns/day.
>You can increase the time step to 2fs by constraining all bonds using LINCS 
>or SHAKE.
>>3- After running the simulation how can I get the position and the speed 
>>of the moleculs (atoms) at each time output?
>Marcus Kubitzki
>Max Planck Institute for Biophysical Chemistry
>Computational Biomolecular Dynamics Group
>Am Fassberg 11
>D-37077 Göttingen
>phone: ++49-551-2012312
>fax: ++49-551-2012302
>Email: mkubitz[at]gwdg.de
>www: http://www.mpibpc.mpg.de/groups/de_groot/
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