AMBER Archive (2009)

Subject: [AMBER] part of the protein escaped from the water box

From: qiaoyan (qiaoyan_at_dicp.ac.cn)
Date: Thu Oct 15 2009 - 06:33:00 CDT

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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