[gmx-users] how to do simulation at high temperature
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 9 10:19:49 CEST 2006
Dongsheng Zhang wrote:
> Dear gmx users,
> I want to simulate a short peptide in solution at high temperature (e.g.
> T=800). Because of the large momentum of molecules, it is very easy to
> have bad contacts to cause the system to crash. One way to prevent it is
> to reduce the time step. Therefore I have tried to use dt=0.0005 with
> hbonds constrains. This is about 4 time slower than T=300k. However, my
> system still crashed. I don't want to reduce the time step too much.
> Could someone to give me an suggestion how to simulate a simple system
> at high temperature? Thank you in advance!
What pressure/density are you using? The velocity of particles at 800 K
is only 1.5-1.6 times larges so you shouldn't need to decrease the
timestep so much.
> Best the wishes!
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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