Re: Colvar distance xy to restrain ions

From: Jérôme Hénin (
Date: Thu Jan 12 2017 - 04:09:12 CST

Hi Azadeh,

To prevent ions from entering a cylinder, you'll need a lower rather than
upperBoundary. And yes, that will require one colvar per ion. If you use a
moderate number of atoms to define each variable, this should still be
efficient, especially if you run on a multicore machine with an SMP-enabled
build of NAMD, in which case calculation of the colvars will be distributed
across cores.

You can check that it is the case by looking for the following line in the
colvars: SMP parallelism is available.


On 12 January 2017 at 09:42, Azadeh Alavizargar <> wrote:

> Hello everyone
> I have a protein-membrane system with lots of ions. I want to prevent the
> ions to enter a hypothetical cylinder aligned with the pore of the protein
> using the upperBoundary of the distance xy of the colvar module. Do I have
> to have a colvar for each ion or there is a way to do it for all the ions
> with a single colvar?
> If not, what is the best way to do it?
> Thank you very much for your help.
> Kind regards,
> Azadeh

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:01 CST