From: Cem Meydan (cemmeydan_at_sabanciuniv.edu)
Date: Thu May 13 2010 - 07:25:30 CDT
Dear NAMD users,
I'd like to use NAMD to perform minimization on some modeled proteins.
However I'm curious if the minimization procedure requires a water box,
whether NAMD uses interactions with water during the energy calculation in
the CG method. I'll not perform equilibration/MD runs afterwards, so it
would be strictly for minimization. Should I omit the solvation/setting up
PBC steps? Would it affect the quality or the speed of the runs in any way?
Thanks.
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