On Sun, Nov 06, 2022, Tanmoy Paul via AMBER wrote:
> It did not work. The error remains the same. Any other tips?
This is not very helpful. What is "it" that did not work? What did you
change? What is the "error" that remains the same? Did you run a zero-step
MD run, as suggested?
...thx...dac
>>> Let's try to narrow down the problem: as an experiment, try a much smaller
>>> buffer, say 8 Ang. instead of 12. This will lead to many fewer atoms. Do
>>> you still see problems? If you do, leave out the water altogether --
>>> let's see if the protein system itself is leading to problems.
>>>
>>> Loading a prmtop file from Amber16 into VMD might not be the best way to
>>> tell if there are problems. Try running a zero-step MD (nstlim=0), and
>>> see if you get reasonable energies, especially (say) for the bonded terms.
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Received on Sun Nov 06 2022 - 14:30:03 PST
