Dear everyone:
I simulate a protein including 104 residues, the protein was surrounded by a periodic box of water molecules described by the TIP3P potential extended to a distance of 10.0A from any solute atom. After 6ns of constant-pressure simulation, part of the protein escaped from the waterbox, I don't know whether this phenomenon affect the result, please help me,thank you!
The script I use 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,iwrap=1.0,
ntc=2, ntf=2,
ntb=2,
ntp=1,pres0=1.0,taup=3.0,
ntt=1, tautp=3.0,temp0=300.0,
ioutfm=1
/
Have a nice day!
qiaoyan
2009-10-15
qiaoyan
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Received on Thu Oct 15 2009 - 05:00:02 PDT
