Re: simulation crashing in 2nd stage equilibration

From: Giacomo Fiorin (
Date: Fri Aug 11 2017 - 07:57:11 CDT

Hi Shivam, did you use fixedAtoms to freeze the protein? If so, you
probably have not minimized its coordinates at all.

I would suggest using position restraints (that are turned on by the
confusing keyword "constraints") starting at minimization, and then
releasing them after some equilibration.

Also, your density may be off depending on your setup procedure, so you
should look into using NPT as well.


On Fri, Aug 11, 2017 at 7:32 AM, <> wrote:

> Dear namd users
> I am simulating protein solvated in water using both oplsAA and charmm
> force field (separately(obviously)) for that i am using following strategy
> : 1st stage equilibration: protein freezed, minimization run : 500, NVT :
> 100 ps
> 2nd stage equilibration : protein free to move, NVT : 100 ps.
> so my problem is 2nd stage equilibration continued from the ouput files of
> 1st equilibration is running fine when i am running using oplsAA force
> field
> but when i am trying to do the same using the charmm force field the
> simulation is crashing giving an error " ERROR: Constraint failure in
> RATTLE algorithm for atom 1164!
> ERROR: Constraint failure; simulation has become unstable."
> why is this happening and how to fix it?
> regards
> shivam

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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