VMD-L Mailing List

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Tue May 29 2018 - 11:04:27 CDT

Hello everyone,

I would like to set up a simulation with a large number of different
distance restraints between atoms. I was wondering how I would be able to
do this.

I have looked at colvars, and it seems to do what I want, however all the
information I can find on it shows distance restraints only between two
groups, and I would like to do maybe around 100 groups. I have also seen a
similar question here (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2006-2007/2185.html
)
on the mailing list and it was saying to use the freeEnergy calculation's
urestraint command, however I just learned that these methods have been
depreciated.

So is there a way to have a large amount of constraints in one colvars
method?

Thank you in advance! 

-- 
Nicholas J. Palmer