From: Ankita Kandalkar (kandalkarankita_at_gmail.com)
Date: Fri Oct 14 2022 - 05:20:57 CDT
Hello to all NAMD users,
I am trying to run a protein-protein molecular dynamics simulation using
NAMD software.
First I have solvated system with 10 angstrom boundary later ionized system
using VMD default parameters then moved on to following steps before the
production run step which are as:
1) Minimization with 50,000 steps
2) Heating with 15,000 steps (heating up to 300K)
3) Equilibration with 50,000 steps (velocity rescaling)
4) Unconstrained Equilibration with 25,000 steps
Finally started the production run. But, I am facing constant errors while
running it. The job stops midway complaining of Constraint failure in the
RATTLE algorithm for atom 5298! There does not seem to be anything unusual
around this atom. But on many repetitions of the same procedure, it's
always the same atom.
I am attaching the production configuration file, error log file, pdb and
psf files(
https://urldefense.com/v3/__https://drive.google.com/drive/folders/1Ft0nDdT4D1S47qkKf4ErywMDqbfF2Vl9?usp=sharing__;!!DZ3fjg!7CIvxRB66ZzedumUuMDoJFdofm7mb-XunULX4DcE7xIHY7NyTBoXaNtgMqnMG5VpILoREBzwKpgrRDipyv_6RpS-0cg$
)
in my google drive. It would be helpful if anyone can guide me to avoid
such errors.
Thank you in advance.
Regards,
Ankita Kandalkar
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