Re: I can not run fixed protein in membrane with NAMD

From: R.L. Ma (
Date: Sat Jun 27 2015 - 21:27:18 CDT

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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