From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jan 09 2009 - 08:54:26 CST
On Fri, 9 Jan 2009, Do Nhu Trang wrote:
DNT> Thanks so much for the suggestions.
DNT> The protocol of Joshua works well with the constraints on whole system with
DNT> the same force and the constraints decrease uniformly as he said. But my
DNT> case is a little bit different. I need to apply the constraints to a part of
DNT> the system and the time of different constraints are different.
DNT> So now, the easiest way I found is splitting the simulation into stages.
DNT> However, by doing so, I have problem in watching the whole evolution of the
why so?? you can easily load multiple trajectory files "on top of each
other" into visualization tools like VMD. not to mention the fact that
with the catdcd tool (bundled with VMD) you can also concatenate
multiple dcd files into one (although in most cases it is convenient
to keep them apart).
DNT> I still need a more graceful and efficient way. Any more suggestion?
-- ======================================================================= 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.
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