From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Feb 23 2017 - 17:36:52 CST
Hi,
Your problem is entirely the number of atoms. if you pick just one atom per
lipid (e.g. a glycerol carbon), you should get the same center position at
a much reduced cost.
Best,
Jerome
On 24 February 2017 at 00:25, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> 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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