From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Tue Oct 30 2007 - 18:10:38 CDT
I'm not sure I understand the problem entirely, but can't you get the
approximate dimensions form the coordinates themselves, i.e. align your
system with the Cartesian axes and calculate the maximum/minimum x, y,
and z values of your system? These would be approximate values that
improve with the size of your system.
Better yet, if your dcd and xst output frequencies match, you should be
able to get the cell info from the xst file.
Victor
On Tue, 2007-10-30 at 21:29 +0200, François Marchand wrote:
> Dear All,
>
> I simulated several systems with NAMD-2.5 (CPT conditions) and I want to
> analyze the trajectories with CHARMM, and specifically I would like to reset
> the correct cell dimensions.
>
> The problem is that I forgot to set the 'DCDUnitCell' option to 'yes', and
> according to
> ( http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4990.html )
> the default option in NAMD-2.5 is 'no'.
>
> My question is: are the cell informations coded somewhere in the NAMD-dcd's or
> are they definitively lost (what I expect...)?
>
> If yes, how can I recover them in CHARMM format?
>
> I tried 'catdcd' and
> 'dcdcellfix' (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2617.html)
> (they set the cell dimension to 1.00 for every frame) and numerous CHARMM
> scripts, but always unsuccessful thus far!
>
> Thanks in advance for an answer!
>
>
> François
>
>
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