I've checked out the mailing list and web regarding this, and there is
the following document in amber website on this matter.
http://ambermd.org/namd/namd_amber.html
For getting the right cellbasisvectors to use in NAMD for a system in
Truncated Octahedron (TO), there is a formulae in this website.
cellBasisVector1 d 0.0 0.0
cellBasisVector2 (-1/3)*d (2/3)sqrt(2)*d 0.0
cellBasisVector3 (-1/3)*d (-1/3)sqrt(2)*d (-1/3)sqrt(6)*d
Is the last term for cellBasisVector3 correct? There is a script in ub.edu
written in perl (called amber2namd.pl) that created namd input files from
amber prmtop/inpcrd files, and in this script the last term is positive;
namely (+1/3)sqrt(6)*d.
Can anyone having an experience on using amber files in namd simulations
comment on this? Thanks.
Best,
Ilyas Yildirim, Ph.D.
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Received on Thu Feb 28 2013 - 16:00:02 PST
