Hi David,
I have provided the files (prmtop, ncrst, rst7 and mdin and
min-1.out/nvt.out outputs from my attempts to run minimization and
equilibration) here
https://1drv.ms/u/s!AqJBrTd9Fp4I20ve2fWaXIaegQ6r?e=Xv5WNd
I did try to generate a mdcrd file for the minimization by adding *nptx = 1*
(and other numbers) at the mdin file and *-x min-1.mdcrd* to the command
line.
However, cpptraj confirms no trajectory is being saved.
"""
> parm ../../setup/x_solv.prmtop
[parm ../../setup/x_solv.prmtop]
Reading '../../setup/x_solv.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
> trajin min-1.mdcrd
[trajin min-1.mdcrd]
Reading 'min-1.mdcrd' as Amber NetCDF
Error: NetCDF file has no frames.
Error: Could not set up 'min-1.mdcrd' for reading.
Error: Could not set up input trajectory 'min-1.mdcrd'
"""
Állan
On Thu, Oct 15, 2020 at 9:10 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Oct 14, 2020, Állan Ferrari wrote:
> >
> >I did try to run the minimization using the CPU.
> >- sander returned after running first half with CG minimization (crashed
> >after switching to steepest descent minimization)
> >
> >Program received signal SIGSEGV: Segmentation fault - invalid memory
> >reference.
>
> Can you create a small example that shows this error? We need to be
> able to reproduce it in order to offer help. It looks like there may be
> something strange with this ligand. Please provide the prmtop, rst7 and
> mdin files you used.
>
> If you can get a segfault after a smallish number of minimization steps,
> try stopping a run right before the segfault, and looking at the
> coordinates to see if there are problems. Use the "check" action in
> cpptraj to look for bad contacts. That might provide some clue, but the
> CPU version should not segfault even with bad potentials.
>
> ....dac
>
>
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>
--
*Állan*
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Received on Thu Oct 15 2020 - 06:30:02 PDT
