From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Aug 11 2017 - 08:31:53 CDT
When a structure is far from equilibrium (i.e. not near an energy minimum),
even small differences in the force field can influence whether it will
fall into a shallow or deep minimum.
On Fri, Aug 11, 2017 at 9:20 AM, <t.shivam_at_iitg.ernet.in> wrote:
> > 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.
> > Giacomo
> > 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
> >> 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
> > http://goo.gl/Q3TBQU
> > https://github.com/giacomofiorin
> 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.
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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