[gmx-users] How to specify .mdp file for position restrained simulation?

[jantonioms J. A. Mondragon S]

you need to run genpr to generate a restrained position file
posresfile.itp with a determined force constant value fc and include
the name file in *.mdp file using define label, for example, run

genpr -f my_molecule.pdb -o posresfile.itp -fc 20

edit *.mdp to include

cpp = /usr/bin/cpp
.
.
.
define= -DPOSRESFILE


On Nov 20, 2007 7:30 AM, Peggy Yao <peggy.yao at gmail.com> wrote:
> Hi,
>
> How to specify the .mdp file in order to run position restrained
> simulation? From the examples I found on the internet, it seems that
> the only difference between the .mdp file for position restrained
> simulation and the one for actual MD simulation is the simulation time
> -- the position restrained simulation is much shorter. Is this
> observation true in general?
>
> If yes, usually, how long is enough for the position restrained simulation?
>
> If not, how to specify the .mdp file for position restrained simulation then?
>
> Thanks a lot!
>
> Peggy
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