AMBER Archive (2003)

Subject: GB simulation on protein (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Fri Mar 07 2003 - 11:13:34 CST

---------- Forwarded message ----------
Date: Thu, 06 Mar 2003 16:56:35 +0100
From: cailliez <Fabien.Cailliez_at_ibpc.fr>
To: amber_at_heimdal.compchem.ucsf.edu
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
why.

Thanks in advance for your help,

Fabien 

--
__________________________________________________________________
Fabien Cailliez                         Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique      e-mail : cailliez_at_ibpc.fr
IBPC    13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________