GB simulation on protein (fwd)

From: <>
Date: Fri, 7 Mar 2003 09:13:34 -0800 (PST)

---------- Forwarded message ----------
Date: Thu, 06 Mar 2003 16:56:35 +0100
From: cailliez <>
Subject: GB simulation on protein

Dear all,

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

Thanks in advance for your help,


Fabien Cailliez                         Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique      e-mail :
IBPC    13, rue Pierre et Marie Curie
75005 Paris
Received on Fri Mar 07 2003 - 17:53:02 PST
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