Re: catdcd error

From: Suresh (
Date: Mon Aug 19 2013 - 08:43:35 CDT

I am not much familiar with the catdcd but i can suggest some thing by reading the error.

Two factors may be possible for the error.
- corrupted dcd files (common frames between two dcd files which have similar number of steps or replacing one dcd file with another). This could occur generally when you run the simulations using shell/python script.
- as suggested previously, there may be no space left on you hard drive.

hope this helps


----- Original Message -----
From: "Revthi Sanker" <>
Sent: Monday, August 19, 2013 5:45:04 PM
Subject: namd-l: catdcd error

Dear all,

I am using the recent version of catdcd( precompiled binany and not as vmd plug-in) using the command:

catdcd -o ptn_20ns.dcd -stride 100 md1_out.dcd md2_out.dcd md3_out.dcd md4_out.dcd

this worked fine for the 2 of my systems and catenated properly.
while for another system it displayed :

dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opened file 'md4_out.dcd' for reading.
dcdplugin) write_dcdstep: error during write
Error writing coordinates frame.

I am not able to get any information on the nature of error. My NAMD log file did not have any warning or error messages either. Kindly suggest what would have gone wrong and how this could be rectified.

Thanks for your help in advance.

M.S. Research Scholar
Indian Institute Of Technology, Madras

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