Re: DCD trajectories produced by SMD simulation

From: Peter Freddolino (
Date: Mon Nov 12 2007 - 11:32:09 CST

Hi Vlad,
I certainly have not noticed this behavior in any of the SMD
trajectories that I've run recently. Could you give a little more
information on where you're running? Also, could you check whether your
jobs are ending in the middle of a write to the dcd? The dcd.bak file
should just contain the same information as the dcd from the previous


Vlad Cojocaru wrote:
> Dear NAMD community,
> I noticed that the DCD trajectories produced by SMD simulation in NAMD
> 2.6 are corrupted (they cannot be loaded properly in VMD 1.8.6).
> Luckily, NAMD creates also a DCD.BAK backup which can be properly
> visualized. This problem is independednt of the trajectory size.
> Is there a fix for this problem ?
> Thanks
> Best wishes
> vlad

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:31 CST