[gmx-users] total time for MDsimulation

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Feb 23 16:36:46 CET 2005


I am surely no expert at assuming the optimal time length of a MDrun, 
but what I can say is, that
1. The position restrained run is for equilibrium of the water (or 
better solvent molecules incl. ions) and in that case not able to be 
included into the whole time scale evaluation
2. 1 ns (and it depends a bit on the system and your goals, I guess) is 
the time one should use as minimum runtime.


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/

shailza singh wrote:
> Dear users,
> i want to know that what is the total time taken for
> simulation of a protein if a protein is run with
> position restrained dynamics with 0.5 ns and without
> position restrained for 1.0 ns? 
> Is the total time accounted will be 1.0 ns only taking
> into account the full MD run or 1.5 ns taking into
> account both short and full MD run?
> Also, I would like to clear about my doubt for full MD
> run?Should it be run for a longer period of time than
> short MD run or we can set the same number of steps as
> that of position restrained dynamics..only barring
> define=-Dposres...
> Any help would be greatly appreciated.
> Thanking you
> shailza.
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