it's hard to say if the structure is ok or not. you might want to visually
inspect it based on your knowledge of the system, especially the ligand.
does it look ok?
are the energies ok in the minimization output? did it get stopped by the
wallclock, or had it gotten stuck before the 24 hours was reached?
On Mon, Oct 5, 2020 at 12:25 PM Jatin Kashyap <jk435.njit.edu> wrote:
> Yes, that is the step. But I am sorry for not bing clear at first, I am
> using my own system instead of Sustiva-RT complex. My HPC allows jobs to
> run for 24 hrs.
> And I am performing minimization for 2000 steps but the last step I can
> see in output file is 1057 before it is terminated my HPC’s job scheduler.
> Can I just go ahead and use the existing .ncrst file for MD run?
>
> Thank you.
>
> ——
>
>
> > On Oct 5, 2020, at 11:38 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> >
> > can you be more specific on which step you mean, and the length of the
> wall
> > clock limit?
> > If you mean the step "Minimize and Equilibrate the Sustiva-RT complex",
> > this should not take very long and you may want to check your output to
> see
> > if it is actually running. For debugging you might want to set ntpr=1
> (but
> > do not do this for production runs).
> >
> > On Mon, Oct 5, 2020 at 11:29 AM Jatin Kashyap <jk435.njit.edu> wrote:
> >
> >> Dear AMBER Community,
> >>
> >> I am following the antechamber tutorial for my system (
> >> https://ambermd.org/tutorials/basic/tutorial4b/index.html).
> >> During the minimization step, the wall clock limit was hit before
> >> completion of the minimization.
> >> Shall it affect the structure of output files, and prevents me from
> going
> >> to next step i.e., equilibration.
> >> Do I have to restart the minimization by decreasing the minimization
> steps
> >> so that it will be finished before hitting the wall limit OR I don’t
> have
> >> to worry about it, and I can continue with existing files, if yes then
> how?
> >>
> >> Thank you.
> >>
> >>
> >> ——
> >> Jatin Kashyap
> >> Ph.D. Student
> >> Dr. Dibakar Datta Group
> >> Department of Mechanical and Industrial Engineering
> >> New Jersey Institute of Technology (NJIT)
> >> University Heights
> >> Newark, NJ 07102-1982
> >> Phone- (201)889-5783
> >> Email- jk435.njit.edu
> >>
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> >>
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Received on Mon Oct 05 2020 - 12:00:02 PDT
