I agree with Dave, it seems likely to be a problem in your scripts on
inputs. Can you share the mdout file for the job that failed?
On Wed, Nov 11, 2020 at 11:24 AM MYRIAN TORRES RICO <
myriam.torres.iiq.csic.es> wrote:
> Hi David,
>
> Sorry but I'm a little lost...
> I did the leap, and it didn't give me any problem, so those
> coordinates are my input files. After the previous step (min and heat)
> did not give me problems either, until step of constant pressure. I
> have been reading that it may be due to problems in the use of CPU or
> GPU, but I have used both pmemd.cuda and pmemd.MPI and it stops ...
>
> how can I check with cpptraj?
>
> Thanks in advance,
>
>
> Myriam
>
>
>
>
> David A Case <david.case.rutgers.edu> escribió:
>
> > On Wed, Nov 11, 2020, MYRIAN TORRES RICO wrote:
> >>
> >> I have a problem with my input in the pcte step. There is a problem
> >> with the initial parameters that do not allow me to converge because
> >> when I launch the script, this error appears:
> >>
> >>
> >> vlimit exceeded for step 0; vmax = **********
> >
> > You have bad coordinates on input. The first step is to use the "check"
> > command in cpptraj to look for bad bonds and close contacts.
> >
> > But a second step is the double-check all your file names. You seem to
> > be doing a restart, so it is somewhat unusual to see a failure on step
> > 0. Do a single step of minimization, and compare the energies to what
> > you had on the final step of the previous run. That might help find
> > some errors.
> >
> >>
> >> Coordinate resetting cannot be accomplished,
> >> deviation is too large
> >> iter_cnt, my_bond_idx, i and j are : 3 889 1785
> 1787
> >
> > Finally, you could look at atoms 1785 and 1787: is the geometry around
> > that area good?
> >
> > ....dac
> >
> >
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Received on Wed Nov 11 2020 - 09:00:02 PST
