Dear Amber users,
I am running a prodution simulation of protein 3TNP in a 10A solvatebox.
After about 25 ns of simlutation time, part of the protein drifts out of
the solvent box. As the protein falls out further it breaks apart
eventually and the fragment comes back in from the other side of the
solvent box. Will I solve this problem by simply increasing the size of the
solvent box? Is there a way to lock the protein within the box? Thanks for
any help!
The input file follows
&cntrl
imin=0, irest=0, ntx=1,
ntpr=2000, ntwx=2000, nstlim=2500000,
dt=0.001, ntt=3, tempi=300,
temp0=300, gamma_ln=1.0, ig=-1,
ntp=0, ntc=2, ntf=2, cut=8,
ntb=1, iwrap=1, ioutfm=1,
/
Regards,
Richard
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Received on Wed Jun 12 2013 - 14:00:02 PDT
