[gmx-users] How to specify .mdp file for position restrained simulation?
leafyoung at yahoo.com
Tue Nov 20 10:43:25 CET 2007
A side note to -DPOSRES, it is actually a C preprocessor defined
variable. There is a corresponding
in the topology file you built. It is default to POSRES, but you can
rename it to other name and change accordingly the "define=.." line in
the mdp file. Also, you can use this mechanism to do position restraint
MD with different parts of the system, or gradually give freedom to the
On 11/20/2007 4:18 PM, Maik Goette wrote:
> 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:
>> 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
>> If not, how to specify the .mdp file for position restrained
>> simulation then?
>> Thanks a lot!
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