Re: Colvar distance xy to restrain ions

From: Azadeh Alavizargar (
Date: Thu Jan 12 2017 - 04:30:42 CST

Dear Jerome

Thanks a lot for your quick response. You are right, I am sorry about that.
I need a lower boundary. Actually, because of the form of my structure, I
need lots of ions, otherwise, I would have kept the ones that neutralize
the system.

I checked my log file, there is no such line for colvar.

There are only these lines for SMP:

Charm++> Running on 1 unique compute nodes (24-way SMP).
CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level
notification) but not using node-level queue

What about using TCLforces? I am not sure if using it would definitely keep
the ions outside the cylinder.

Thank you very much again for your time and help.


On Thu, Jan 12, 2017 at 1:39 PM, Jérôme Hénin <> wrote:

> 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
> output:
> colvars: SMP parallelism is available.
> Best,
> Jerome
> 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

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