Date: Mon Jun 13 2005 - 01:51:35 CDT
The trouble is, you're trying to go directly from an energy-minimized system
(i.e., one at absolute zero temperature) to a room-temperature system.
Generally MD codes aren't meant to be used that way... the sudden influx of
kinetic energy will make things unstable. Have a look at the tutorials
(and/or search this list) for some hints on how to *heat* your system a bit
more gradually. (For example, I usually run something like 20 to 50 ps of
heating dynamics, in order to smoothly go from 0 to 300K.)
Hope this helps.
C. Erik Nordgren, Ph.D.
University of Pennsylvania
Quoting Shirley Hui <shirleyhui_at_alumni.uwaterloo.ca>:
> I am running a simulation and for some reason, the simulation seems to be
> stopping prematurely, usually a few timesteps into the simluation after
> The errors are:
> ERROR: Constraint failure in RATTLE algorithm for atom 2038!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
> I saw another posting for a similar problem here:
> As suggested I viewed the DCD file in VMD for the minimization but nothing
> seems to be wrong.
> I've included the configuration file, and the out put file here:
> Config file:
> PDB file:
> PSF file:
> OUTPUT file:
> Thanks for any help.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:50 CST