From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Oct 30 2007 - 16:14:02 CDT
Hi François,
If you didn't set DCDUnitCell to 'yes' in NAMD 2.5 the information about
the cell is unfortunately lost. In NAMD 2.6 the default was changed to
'yes'. If your cell was cubic and you have saved NAMD output you might
retrieve it from there. NAMD prints the information about the total volume
of the cell and by calculating the cubic root (if your cell is cubic) you
can get the side length. Otherwise I fear there is no other way to
retrieve it.
Greetings,
Gianluca
On Tue, 30 Oct 2007, 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
>
>
> --
> ________________________________________________
> François Marchand
> Department of Biochemistry, Caflisch Group
> University of Zurich, Winterthurerstrasse 190
> CH-8057 Zuerich / Switzerland
>
> Phone +41 1 635 55 59
> Fax +41 1 635 68 62
>
>
-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4435
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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