From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Fri Oct 08 2010 - 11:30:36 CDT
On Friday 08 October 2010 16:07:08 you wrote:
> I've used the dumpdcd.c program in the NAMD src directory to look at the
> headers of the truncated files. The two dcd files I've looked at
> (npgt322.dcd and npgt232.dcd) appear to have been processed by some
> program that claims to be CHARMM 34, but NAMD pretends to be CHARMM 24.
> Do you have the original dcd files output by NAMD?
Well, the setup and the PSF, PSF.EXPLOR, and PDB files were generated with
CHARMM 34b2. But the all runs where run with namd 2.7b2 Linux-x86_64-net-
I just did some analysis with CHARMM but only opened the dcd files for
reading. I never did changes to the original files produced by NAMD.
To answer you second question:
> If that is the pattern then you should be able to reproduce the truncation
> effect by repeating an earlier run. Have you tried this?
I restarted from run051 and run052 successfully completed. Same for the other
I am kind worried that it really will re occur at run412.
Thanks for your help.
-- Bjoern Olausson Martin-Luther-Universitšt Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
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