From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Feb 23 2017 - 17:25:14 CST
Hello,
I am doing solute tempering simulations with a POPC/peptide system using
NAMD 2.10. To the best of my knowledge, this is the only version of NAMD
that can work with the REST2 implementation (Jo and Jiang, JCTC, 197:304,
[2015])
I also have 3 colvars to prevent my peptide from interacting with the
lipids in the periodic image along Z dimension. These are distance colvars,
defining the distance of the N-terminal residue, center residue, and
C-terminal residue with the lipid heavy atoms. Number of atoms in each
colvar is ~ 10500.
>From what I understood from the following link, it is the number of colvars
and not number of atoms in a colvar that could affect the scaling, correct?
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/1135.html
Has anyone else faced this issue? And any suggestions on how best to
address this? Would using the absolute Z value of the residues as the
colvar give the same effect with a better scaling?
Thanks and regards,
Chitrak.
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