Re: GB simulation on protein (fwd)

From: David A. Case <>
Date: Fri, 7 Mar 2003 10:02:13 -0800

On Fri, Mar 07, 2003, wrote:
> I tried to carry a simulation of a protein with the version 7 of Amber
> using GB solvent representation (igb=1,
> saltcon=0.1, offset=0.13, cut=50).
> After only 1 ps of heating, some atoms began to have v > vlimit (even v
> = NAN) and
> the calculations stopped because shake cannot be accomplished (deviation
> too large).
> As I had no such problems carrying the simulation of the same protein
> with explicit water molecules (same
> protocol), I am wondering why my system crashed.
> I suppose it is due to the GB solvent representation but I do not know
> why.

Sounds like to you need to minimize before starting the MD. If that doesn't
help, heat very slowly, print out the energies at every step, see if you
can figure out what is going on. Be sure to heat up first with positional
restraints before allowing the protein to go whereever it wants.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Fri Mar 07 2003 - 18:53:01 PST
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