[gmx-users] position restrained dynamics & protein size

Erik Marklund erikm at xray.bmc.uu.se
Tue Jan 19 11:22:11 CET 2010


If we're really talking about timestepe here, then position restraints 
have no impact as far as I know. If, on the other hand, we're talking 
about total simulation time, then the size of your system will affect 
the time required to relax the structure. In the end it depends on what 
protein you're simulating. Is there anything in the literature about the 
timescales of water dynamics for your protein. 3666 atoms is not that 
big, so I think you could play it safe and simulate a bit longer, say 
500 ps, although 100 ps is often enough.


rituraj purohit skrev:
> Dear friends,
> I am working to study dynamic behaviour of a protein molecule, having
> 3666 atoms. My question is related to position restrained dynamics
> step.
> What should be the time step in position restrained dynamics ?
> This time i am giving 100ps, but i don't know is it sufficient to sock
> the water in protein cavities.
> Is their any relationship between position restrained dynamics time
> step and protein size?
> Please advise me.
> Regards
> Rituraj

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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