[gmx-users] Few general questions.

Anton Feenstra feenstra at chem.vu.nl
Tue Sep 16 09:07:03 CEST 2003


In addition to Davids reply, a few more tips and remarks:

Itamar Kass wrote:
>    Dear all, I am working with GROMACS for some time, and I have gather some
> questions. I will appreciate if someone will have the time to answer my questions.
> 1.When I run mdrun I use the flag -v to see the time left until the simulation

There also is a hidden flag to mdrun (try 'mdrun -h -hidden') to reduce the number
of times the time left is written. Default this is every 10 steps, but for a long
simulation, you may only want it every 1000 steps or so. This will help keep your
log files small... ;-)

> 2.I work upon a system of a peptide embedded in a membrane, what is the largest
> time step I can use?  For now I use time step of 2fs, although I saw other use
> time step of 5fs (for membrane), is it O.K. To use such large time step?

As David suggested, read one of my papers: J. Comput. Chem. 20 (8), pp 786-798, 1999
There are two tricks involved which are more or less independent:
1) increase hydrogen mass (at the expense of a heavy atom) to reduce vibrational frequency
2) eliminite hydrogen degrees of freedom by additional constraints or dummy atom
Both are included as options to pdb2gmx (-heavyh (?), and -dummy hydrogens/aromatics)

> 3.Connected to the previous question, how do I know if the SHAKE/LINCS
> algorithms work?  How can I activate/deactivate them if I want to (using the mdp
> option or mdrun flag)?

Both Shake and Lincs will issue warnings if things start to go wrong, and
halt the simulation if it really goes bad.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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