From: nordgren_at_sas.upenn.edu
Date: Mon Jun 13 2005 - 01:51:35 CDT
Dear Shirley:
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.
- Erik
C. Erik Nordgren, Ph.D.
Chemistry Department
University of Pennsylvania
Quoting Shirley Hui <shirleyhui_at_alumni.uwaterloo.ca>:
> Hi,
> I am running a simulation and for some reason, the simulation seems to be
> stopping prematurely, usually a few timesteps into the simluation after
> minimization.
> 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:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0042.html
>
> 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:
> http://www.cs.uwaterloo.ca/~s2hui/dropbox/cll.namd
>
> PDB file:
> http://www.cs.uwaterloo.ca/~s2hui/dropbox/cll-solvate.pdb
>
> PSF file:
> http://www.cs.uwaterloo.ca/~s2hui/dropbox/cll-solvate.psf
>
> OUTPUT file:
> http://www.cs.uwaterloo.ca/~s2hui/dropbox/test.log
>
> Thanks for any help.
> shirley
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