Re: NAMD 2.6 dcd and breaking XPLOR

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 14 2008 - 07:14:02 CST

I can verify that aside from the change in header, the 2.6 dcds actually
are storing unit cell information throughout the simulation, which is
useful for a number of reasons (most notably, it allows you to properly
postprocess a trajectory with pressure control, without digging into the
xst). I'm not familiar enough with xplor to know whether it isn't
compatible with dcds that have this information, or if there's some
option that needs to be turned on to allow it to read them. This is,
however, why just modifying the header isn't helping.
Catdcd may help both because it lets you extract pdb frames from dcds,
and may be able to write a different trajectory format that xplor
understands if you need to do something else in xplor. Jim may have
further input; I don't know the dcd format, so I can't comment on the
exact details of what program supports what features.

Best,
Peter

Neema Salimi wrote:
> Using wordom (http://www.biochem-caflisch.unizh.ch/wordom/) to read
> the DCD headers, I have discovered that NAMD 2.6 headers are different
> from 2.5 headers using the same input files. The 2.5 DCDs invariably
> have the "Variable PBC" line set to "0", while the 2.6 DCDs have the
> same line set to "1". Unfortunately, using wordom to modify the DCD
> header doesn't solve the problem. I can use wordom to process the DCD
> files, so I know they're not completely screwed up. Does ANYONE have
> any insight?
>
>
> On Feb 7, 2008, at 3:15 PM, Neema Salimi wrote:
>
>> Did NAMD 2.6 break dcd files for reading into XPLOR? I use XPLOR to
>> do a few things, like extract PDBs from NAMD's binary dcd files. I
>> recently switched to 2.6, and now XPLOR complains that there's no
>> coordinate sets inside the dcd file. My guess is that is has
>> something to how the frames are indexed, but I haven't been able to
>> work it out just yet. And yes, my simulations are running fine, I
>> can convert binary coordinate restart files and the energy outputs
>> look normal. Thanks.
>>
>> Neema Salimi
>> nsalimi_at_msg.ucsf.edu <mailto:nsalimi_at_msg.ucsf.edu>
>>
>> University of California-San Francisco
>> Graduate Group in Biophysics
>> Agard Lab
>> http://msg.ucsf.edu/agard/
>> Lab Phone: (415) 476-5143
>>
>>
>>
>>
>
> Neema Salimi
> nsalimi_at_msg.ucsf.edu <mailto:nsalimi_at_msg.ucsf.edu>
>
> University of California-San Francisco
> Graduate Group in Biophysics
> Agard Lab
> http://msg.ucsf.edu/agard/
> Lab Phone: (415) 476-5143
>
>
>
>

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