Since you asked if it was "correct", I would add to Jason's suggestion that
igb=1 is a model with known serious weaknesses. You will need to proceed
cautiously, check the results against experiment, and expect problems. It's
impossible to give any more specific advice since you haven't said anything
about what you're actually trying to learn.
On Apr 4, 2014 7:29 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
> On Fri, 2014-04-04 at 12:47 +0200, Urszula Uciechowska wrote:
> >
> > Dear amber users,
> >
> > I am running MD for DNA+protein, in one of my input I would like to use
> > igb=1, below is my input file. Could someone have a look at it at check
> if
> > its correct? I have never done Md for igb=1 before.
> >
> > production
> > &cntrl
> > imin = 0, irest = 1, ntx = 7,
> > ntb = 0, ntp = 0,
> > taup = 2.0, igb = 1,
> > cut = 12, ntr = 0,
>
> This cutoff is way too short for GB simulations in my opinion. I
> usually set cutoffs to ~1000 A ( equivalent to no cutoff) for GB
> simulations.
>
> > ntc = 2, ntf = 2,
> > tempi = 298.15, temp0 = 298.15,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 250000, dt = 0.002,
> > ntpr = 200, ntwx = 200, ntwr = 200
>
> YOu are probably printing out energies, restarts, and coordinates too
> frequently (especially if you are using a GPU).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> 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
Received on Fri Apr 04 2014 - 05:00:02 PDT
