VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Sep 07 2007 - 07:56:23 CDT

On Fri, 7 Sep 2007, maria goranovic wrote:

MG> Hi,

hi maria,

MG> Is it possible to skip (say) the first 500 frames of a trajectory when using
MG> bigdcd to analyze a large trajectory ?

yes.

MG> something like ...
MG>
MG> bigdcd myprodecure mytraj.dcd skip 500 ?

not like this though, since all arguments to bigdcd are
assumed to be names of dcd files.

however, if you locate the line with
'animate read dcd $dcd waitfor 0'
in your bigdcd.tcl script and only use one dcd file,
you can just change that line to
'animate read dcd $dcd beg 500 waitfor 0'
and you should get what you desire.

if you want to run through multiple files, the hack
has to be a little bit more elaborate. please let us
know if you need more help.

alternatively, you could use the catdcd tool to cut
away the first part of your dcd file. see.
http://www.ks.uiuc.edu/Development/MDTools/catdcd/

cheers,
   axel.

MG>
MG> Thank you for the tips
MG>
MG> Maria
MG>
MG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.