From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Jun 29 2015 - 14:41:11 CDT
How did you "fix" the protein? Have you verified whether your cell
dimensions are still the same (i.e. you can continue to use the PBC from
the previous configuration file)?
On Sat, Jun 27, 2015 at 10:27 PM, R.L. Ma <marulong2013_at_gmail.com> wrote:
> Hi the developers of NAMD:
> I am doing a research with NAMD 2.9 and have a problem about it,
> could you give me a favor? I have done molecular dynamics simulation of a
> membrane-protein with solvent and it ran normally. And then I selected a
> frame from the molecular trajectory and got its pdb file, I wanted to fix
> the protein and did the second molecular dynamics from this pdb file, (the
> configuration file were not changed except fixing protein,) but it failed,
> the error is that atoms move too fast, the last part of the log is as
> ERROR: Atom 46395 velocity is -61060.6 17697.8 -16340.7 (limit is 6000,
> atom 892 of 903 on patch 61 pe 1)
> ERROR: Atom 46543 velocity is -7952.35 8551.18 402.814 (limit is 6000,
> atom 899 of 903 on patch 61 pe 1)
> ERROR: Atoms moving too fast; simulation has become unstable (104 atoms on
> patch 61 pe 1).
> ERROR: Exiting prematurely; see error messages above.
> I have attempted other membrane-protein and it has the same errors. I
> will appreciate it if you can help me, thank you in advance!
> Best wishes to you.
> Yours Rulong Ma
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