It should be ok if the parameters are from gaff and not anything that you
set by hand. It's possible, though, that some elements aren't treated well
with the igb=1 solvent model. You would want to consider that based on what
you are simulating, and perhaps use explicit water.
also I would suggest using shake in your simulations, and perhaps doing
equilibration in sander rather than pmemd, and switch to pmemd for
production runs. I also avoid the Berendsen thermostat and use Langevin
instead.
On Thu, Apr 18, 2019, 9:23 AM An Ta <anta.mymail.mines.edu> wrote:
> Dear Carlos,
>
> (1) I have performed a minimization before the heating simulation.
>
> (2) I am using charge-modified GAFF parameters for most of my components.
> But I am not sure if this qualifies as 'unusual'. Is there an approach that
> I can implement to identify which of my parameters may be causing the
> instability or will I have to do the classic 'brute force' approach where I
> check each and every parameter sequentially?
>
> Thank you for all your help,
>
> *An Tien Ta*
> Chemistry Ph.D Candidate
> Colorado School of Mines || Department of Chemistry
> Coolbaugh Hall, Rm. 118
> Golden, CO 80401
> anta.mines.edu
>
>
> On Thu, Apr 18, 2019 at 7:04 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 1) did you minimize first? This is usually needed.
> > 2) do you have any unusual force field parameters? That is often the
> > problem with instabilities.
> >
> > On Thu, Apr 18, 2019, 8:49 AM An Ta <anta.mymail.mines.edu> wrote:
> >
> > > Dear fellow AMBER users,
> > >
> > > I have been attempting to heat up a system in different heating stages
> > > (e.g. (1) Heat from 0-50K, (2) Heat 50-100K, and so forth). But I
> noticed
> > > in my output file that the temperature is exceeding what I have
> specified
> > > for the heating simulation. This is my first time trying to heat a
> system
> > > up and I was wondering if I may have specified some parameter
> > incorrectly.
> > > I have attached my input file and a corresponding output for reference.
> > >
> > > Thank you for your time and any advisement,
> > >
> > > *An Tien Ta*
> > > Chemistry Ph.D Candidate
> > > Colorado School of Mines || Department of Chemistry
> > > Coolbaugh Hall, Rm. 118
> > > Golden, CO 80401
> > > anta.mines.edu
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Apr 18 2019 - 09:00:05 PDT
