Date: Fri Aug 11 2017 - 08:20:42 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, <t.shivam_at_iitg.ernet.in> 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
>> : 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
>> 1st equilibration is running fine when i am running using oplsAA force
>> 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?
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
Dear Dr. Fiorin
Thank you for your suggestions, you are right, i used fixedatoms command
to freeze my protein, i will use NPT after this 2nd stage of
equilibration, but what's bothering me is that, why didn't this error
showed up when i used opls force field on the same system.
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