Re: A problem with intermediate files

From: J. Rui Rodrigues (
Date: Tue Nov 11 2003 - 07:46:33 CST

You can still read your .coor file in VMD: just load your psf file and then
load your .coor file as namdbin.
If you want to continue your simulation, you can use the namd commands
binvelocities and bincoordinates to read your binary .vel and .coor files.

Rui Rodrigues

Zhilei Chen <> escreveu:


 I was using namd to run a 60ps free simulation. At the end of the simulation,
 I successfully obtained the .dcd file and .log file. Everything is normal.
 when I try to use the .coor file it generated, I found it only contained some
 strange code that the vmd can't interprete. I checked the other intermediate
 files (.vel, .restart.vel.old, .restart.vel, .restart.coor,
 and all those contained the same strange code and they all have the same file
 size 1,063,600. I am not sure what is the problem. I tried running the script
 again, used a different name, but exactly the same thing happened. All those
 files still have 1,063,600 as the size and have the same mysterious code in
 it. And again, the .dcd file looked normal and I can open it with VMD. I
 examined the .log file, and it didn't have any warning or error message
 concerning writing these intermediate files.

 I need to use the .coor and .vel for my next simulation. Can anyone tell me
 what's the problem?


J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra

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