AMBER Archive (2009)

Subject: [AMBER] is rst file the last structure?

From: qiaoyan (qiaoyan_at_dicp.ac.cn)
Date: Fri Nov 13 2009 - 22:52:40 CST

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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