VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Feb 23 2009 - 19:00:55 CST

On Tue, 24 Feb 2009, Mohamed Seyam wrote:

MS> Hello,
MS>
MS> I am trying to add a water box around a double stranded DNA, and I was
MS> wondering if you can specify the number of water molecules to put around the
MS> DNA? I would like to add 1748 water molecules around the double strand.

not sure why you need the magic number of 1748, but why don't
you just add more water and delete excess ones somewhere on the
outside of the box. you'll have to shrink and equilibrate the
system anyways.

cheers,
   axel.

MS>
MS> Thanks,
MS>
MS> -Mohamed Seyam
MS> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.