[gmx-users] General Questions abdout gromacs

[Haberl Florian]

Hi,

> Dear all
> I have some questions about gromacs:
> 1- I'm accessing a linux cluster from my PC at my office, when I run a
> simulation I have to keeb the PC on up to the end of the run (which takes
> 10
> days sometimes) is there any command in gromacs which enable me to run the
> simulation from my PC and keep it working in the cluster no matter wither
> my
> PC is on or off?

You can send your job into the background, or start it in a screen.
http://www.cpqlinux.com/jobcontrol.html
man screen

Other and better solotion is to install a queing system:

http://www.clusterresources.com/pages/products/torque-resource-manager.php
http://www.clusterresources.com/pages/products/maui-cluster-scheduler.php

or openpbs but it^s deprecated


> 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?
> 3- After running the simulation how can I get the position and the speed
> of
> the moleculs (atoms) at each time output?
> 4- can I incert a hydrophopic serface into my simulation box? I mean cam I
> make one of the simulation box faces a hydrophopic surface, I'm willing to
> use Gold as  my substrate.




>
> kind regards
> Sven
>
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Greetings,

Florian


------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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