Re: DCD trajectories produced by SMD simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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
timestep...

Best,
Peter

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
>
>
>

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