Hi Bill,
Thank you very much for your reply.
I have equilibrated my system for 5ns with NPT ensemble without restraints. yes, I run in parallel. The following is my input file for equlibration:
villin:5ns MD
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 2,
ntp = 1,
pres0 = 1.0,
taup = 2.0,
cut = 12.0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 2500000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
I will rerun my system to see whether this is helpful.
Thanks in advance.
Jianing
ÔÚ2010-04-13 02:13:25£¬"Bill Ross" <ross.cgl.ucsf.edu> дµÀ£º
>How did you equilibrate before the 2 'equivalent' runs?
>If running in parallel, runs can diverge because of different order
>of execution involving timing of interprocessor communication. Such
>divergence may be more extreme in a simulation that wasn't well-
>equilibrated first. It could be interesting to re-run one of the
>existing trajectories, and see how it compares to the original run.
>
>Bill
>
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Received on Mon Apr 12 2010 - 22:30:02 PDT
