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

Maik Goette 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 
you're standing...

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
37077 Goettingen
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:
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> .

More information about the gromacs.org_gmx-users mailing list