dear all:
the script I used in npt simulation is as follows:
&cntrl
imin=0,
ntx=5, irest=1,
ntpr=100, ntwx=1000,ntwr=5000,
dt=0.002,nstlim=1000000, nscm=1000,
cut=9.,dielc=1.0,
ntc=2, ntf=2,
ntb=2, iwrap=1.0,
ntp=1,pres0=1.0,taup=3.0,
ntt=1, tautp=3.0,temp0=300.0,
ioutfm=1
/
I use the rst file to generate the pdb file a, I think a is the structure of 2ns(the 1000th strcture), then I use ptraj to generate the 1000th structure (trajin nptm501.dcd 1 1000 1000,trajout b.pdb pdb), but when I compare the two structures a and b, they differ significantly. what is wrong with the problem?
2009-11-14
qiaoyan
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Received on Fri Nov 13 2009 - 21:00:02 PST
