Lin, thank you for your response. I will be sure to refer to that tutorial
link from now on and include the 'nmropt' parameter.
Carlos, Thank you so much for all your advisement. Your suggestions
are very helpful and I will keep them in mind for future simulations.
Respectfully,
*An Tien Ta*
Chemistry Ph.D Prospect
Colorado School of Mines || Department of Chemistry
Coolbaugh Hall, Rm. 118
Golden, CO 80401
anta.mines.edu
On Thu, Apr 18, 2019 at 9:44 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
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> > > >
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Received on Thu Apr 18 2019 - 11:00:03 PDT
