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 - 08:30:02 PST
