Re: ion moving laterally during Umbrella Sampling?

From: Giacomo Fiorin (
Date: Tue Oct 03 2017 - 15:16:01 CDT

You can split configuration for different variables in multiple files, and
load them using "cv configfile" or even put them as strings (between double
quotes) in the NAMD main script and load them through "cv config".

Keep in mind that if you put restraints that affect the ion conduction
pathway, you have to question yourself whether you are changing the
resulting PMF, which has to assume a minimum free energy pathway.


On Tue, Oct 3, 2017 at 1:45 PM, Olya Kravchenko <> wrote:

> Hi all,
> in my current umbrella sampling simulations for ion permeation through the
> channel I see ion shifting off the center line (where it supposed to be
> located) near the entrance or exit of the pore (no shift in the windows
> inside the pore). It seems to move to the nearest strong residue and stay
> there throughout simulation without returning back to the specified centre.
> The ion can move 2-3 A to the side over the first 0.5-1 ns and linger there
> for the rest of the simulation. I use distance colvar for this simulation.
> I would expect that for umbrella sampling the ion should not shift that
> far from a specified location (and I haven't seen this in my previous US
> simulations on a similar system). What would be the reason for this to
> happen in US simulations?
> I want to try using distanceXY colvar to restrain this movement. Is is
> applicable in this case, in addition to distance colvar (i.e., not
> distanceZ, but distance)? Do I have to have a separate input file for
> distanceXY colvar or can I add it into the same *.in file as I have for
> distance colvar?
> Thanks in advance, I appreciate your advice.
> Olga

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:41 CST