Dear Amber users,
I have run pmemd of amber 11 on a large protien-DNA system, and found that the complex move out of water box after ~20 ns, leading to very strange RMSD in the trajactory. Could you help me to this problem? How can I keep the center of mass of protein-DNA in the center of box?
parameters I used in the running
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Production MD
&cntrl
imin=0, irest=1, ntx=5, IG=39727,
nstlim=100000000,dt=0.002, ntc=2,ntf=2,
ntpr=5000, ntwx=5000,
cut=8, ntb=2, igb=0,ntp=1, iwrap=1,
ntt=1, tempi=298.0, temp0=298.0,tautp=2.0,
/
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Received on Fri Apr 05 2013 - 00:00:02 PDT
