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!
Dongsheng
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David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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