AMBER Archive (2003)

Subject: Re: GB simulation on protein (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 07 2003 - 12:02:13 CST

On Fri, Mar 07, 2003, amber_at_heimdal.compchem.ucsf.edu 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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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