[gmx-users] How to specify .mdp file for position restrained simulation?
mgoette at mpi-bpc.mpg.de
Tue Nov 20 09:18:09 CET 2007
Use the following term in your mdp:
define = -DPOSRES
Now, everything is true, depending on the question you ask and the point
What you may mean is the following:
POSRES-Sims are mostly (not always) used for equilibrating the solvent
around the protein. These simulations are in general quite short,
because relaxation of water happens quite fast.
In this case a Posres-Sim is much shorter (say 200ps or so) than a
"real" run (usually in the range of ns).
Please be aware, that there is also a parameter file for
position-restraints (e.g. posre.itp), which, if automatically generated
by pdb2gmx contains the positions of all heavy atoms with a force
constant for x,y,z.
And now a suggestion. Please, before starting MD inform yourself about:
a. The theoretical aspects of molecular dynamics
b. The program you are using (i.e. the manual)
The probability of getting good results and no crap increases
dramatically with following the two points above...
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Peggy Yao wrote:
> 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!
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