PBC box problems

From: Michael Ford <mford_at_ccrc.uga.edu>
Date: Wed 28 Feb 2001 17:34:36 -0500

Hello all,

I am having a very difficult time with PBC conditions for a protein
complex. I am attempting to take some minimized coordinates from the
protein + box and do simmulated annealing. I know that the box
coordinates can change (in constant P situations) and I think this is
the case. As soon as I start the simmulated annealing, my protein is
distorted, and I'm guessing it has to do with the transfer of box
coordinates. The box coordinates from the topology file and the
minimization output are the same. Here's my input, let me know if you
can help.

Thanks,

Mike Ford
University of Georgia

minimization:
Complete optimization solute and solvent
 &cntrl
    imin=1, maxcyc=15000, ibelly=1,
    scee=1.2, idiel=1, cut=8.0,
    nsnb=20, ntpr=50, ntp=2, ntb=2,
 &end
Belly definition
RES 27 32
RES 40
RES 43 47
RES 49 54
RES 56 62
RES 64 72
RES 107
RES 110
RES 134 4798
END
END

Simulated annealing
Complete optimization solute and solvent
 &cntrl
    imin=1, maxcyc=15000, ibelly=1,
    scee=1.2, idiel=1, cut=8.0,
    nsnb=20, ntpr=50, ntp=2, ntb=2,
 &end
Belly definition
RES 27 32
RES 40
RES 43 47
RES 49 54
RES 56 62
RES 64 72
RES 107
RES 110
RES 134 4798
END
END



--
ࡱ
Received on Wed Feb 28 2001 - 14:34:36 PST
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