From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jan 12 2017 - 04:40:41 CST
For good performance with many ions, your best bet is TclBC. For that I
would add some positional restraints on the protein, so that the cylinder
is fixed in space and you only need coordinates for the ions.
On 12 January 2017 at 11:30, Azadeh Alavizargar <
> 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 <jerome.henin_at_ibpc.fr>
>> 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.
>> On 12 January 2017 at 09:42, Azadeh Alavizargar <
>> azadeh.alavizargar_at_gmail.com> 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,
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