[gmx-users] Re: cpp default location for mac osX in .mdp files

Anton Feenstra feenstra at chem.vu.nl
Thu May 15 13:09:00 CEST 2003

Ing. Vojtěch Spiwok wrote:
> I suppose that most gmx users have a couple of .mdp files (a kind
> of cookbook) eg. one for minimisation, one for MD with cut-off
> electrostatics, one for MD with PME etc. and for each simulation
> they just copy them to a given directory, rename and modifie them
> for specific purpouse so you need to modify cpp location only in
> these "cookbook" files.

Yes - that is how I usually do it. I also have a scheme with one
'mother.mdp' file, which is modified automatically (by a script)
for EM, MD, position restraints, inclusion of solvent, nsteps, etc.
That is to make sure all other parameters (cut-off, T/P coupling
etc.) are identical between the different runs.

> The cpp location in mdout.mdp file is
> based on mdp input of grompp (I hope!)


> and mdout.mdp file
> only reviews the input of grompp as it contains all parameters
> (including default ones).

Right. When I use a modified .mdp file for the first time, I always
compare my input .mdp file against the mdout.mdp (using e.g. diff or
xdiff), to see whether grompp has interpreted everyting as I want it.

> I think (but I'm not sure) that cpp is only
> necesary for grompp but not for mdrun.

Right: grompp uses cpp as the first stage in processing your .top and
.itp files. Other than that, it is not used (certainly not by mdrun).


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
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