RE: problem when heating the system

From: Pijush Ghosh (
Date: Tue Aug 30 2005 - 00:09:08 CDT

One of my suggestions would be to heat the system in steps, say of 50K or
100K. We had problem with pressure once and then we did it in steps. This is
useful particularly for complex systems.
Another thing I would suggest you to check is the dimension of your PBC.
Make sure it is not smaller than the dimension of your system.
May be somebody can come up with more suggestions.

Good Luck !!!!


Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA
-----Original Message-----
From: [] On Behalf
Of Phoenix
Sent: Monday, August 29, 2005 11:08 PM
Subject: namd-l: problem when heating the system

Hi all,
I got a problem when I heating a system to 298k.After I minimize the system
10000 steps keeping the protein fixed and allowing the movement of the water

box.I want to heat the system to 298k in 20000 steps and occur the
problem.How could I do to solve the problem? attched is my config file

ERROR: Atom 47 velocity is 14541.4 -2450.69 -6229.53 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.

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