Right, thank you!
I am going to carry out some tests, I suppose the problem was related
to the re-imaging of the system. Otherwise, what options may be useful
for NMA section to overcome problems related to minimization?
Cheers,
Enrico
Il giorno mar 9 ago 2022 alle ore 16:17 Ray Luo <rluo.uci.edu> ha scritto:
>
> Enrico,
>
> "Line minimizer aborted" is related to your nmode option, so I don't
> think it's MPI related. You may want to test run a few snapshots with
> the serial mode to make sure the setup is correct before the MPI
> production run.
>
> Finally, please make sure your systems are correctly stripped before
> running again.
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Tue, Aug 9, 2022 at 12:13 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
> >
> > Just finishing some tests I got the error on the step of the
> > calculation of dG for the complex:
> > Line minimizer aborted: step at upper bound 0.14208831
> > File "/home/gleb/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
> > app.run_mmpbsa()
> > File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/main.py",
> > line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
> > line 82, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
> > line 321, in run
> > Calculation.run(self, rank, stdout=self.output % rank)
> > File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
> > line 156, in run
> > raise CalcError('%s failed with prmtop %s!' % (self.program,
> > CalcError: /home/gleb/amber22/bin/mmpbsa_py_nabnmode failed with
> > prmtop complex.prmtop!
> > Error occurred on rank 46.
> >
> > Fatal Error!
> > All files have been retained for your error investigation:
> > You should begin by examining the output files of the first failed calculation.
> > Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> > manual for file naming conventions.
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 46
> >
> > may it be related to the open mpi problem or rather something wrong
> > with the system ( I run it on the system that had not been
> > reimaged..)?
> >
> > Il giorno lun 8 ago 2022 alle ore 19:20 Ray Luo <rluo.uci.edu> ha scritto:
> > >
> > > Hi Enrico,
> > >
> > > Here are my suggestions regarding your questions ...
> > >
> > > > 1) Dealing with the modeling of the dimeric protein where the ligand
> > > > is bound to one of the monomers, do I need to re-image my system prior
> > > > to the post-processing (avoiding jumping parts of the protein across
> > > > the PB) ?
> > >
> > > Yes you'll need to make sure all proteins are in the primary cell
> > > before stripping waters/ions etc. To make sure the system looks right,
> > > I strongly recommend visualizing the stripped trajectories before
> > > running the job.
> > >
> > > > 2) What snapshot density is required for the calculations? For
> > > > example, dealing with the 150ns trajectory where each snapshot was
> > > > saved every 25000 steps, I have around 6000 snapshots. In order to
> > > > speed up the analysis, would it be OK to take each 5th snapshot for
> > > > the calculations of dH and each 10th for the dS ?
> > >
> > > In general, you can use fewer snapshots to save time. The con is that
> > > you'd get higher uncertainties, i.e. standard errors.
> > >
> > > All the best,
> > > Ray
> > > --
> > > Ray Luo, Ph.D.
> > > Professor of Structural Biology/Biochemistry/Biophysics,
> > > Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> > > Biomedical Engineering, and Materials Science and Engineering
> > > Department of Molecular Biology and Biochemistry
> > > University of California, Irvine, CA 92697-3900
> > >
> > > On Mon, Aug 8, 2022 at 7:49 AM Enrico Martinez via AMBER
> > > <amber.ambermd.org> wrote:
> > > >
> > > > Here is my script
> > > > &general
> > > > startframe= 1, interval=${int}, keep_files=2,
> > > > strip_mask=:WAT:Cl-:Na+:K+, netcdf=1
> > > > /
> > > > &gb
> > > > igb=5, saltcon=0.150,
> > > > /
> > > > &nmode
> > > > nmstartframe=1, nminterval=5, nmode_igb=1, drms=0.05, nmode_istrng=0.15,
> > > > /
> > > > &decomp
> > > > idecomp=1,
> > > > dec_verbose=1,
> > > > /
> > > >
> > > > Many thanks in advance!
> > > > Cheers
> > > > Enrico
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
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Received on Tue Aug 09 2022 - 08:00:22 PDT
