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.
Best,
Jerome
On 12 January 2017 at 11:30, Azadeh Alavizargar <
azadeh.alavizargar_at_gmail.com> wrote:
>
> 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.
>
> Best,
> Azadeh
>
> On Thu, Jan 12, 2017 at 1:39 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> 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 <
>> 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,
>>> Azadeh
>>>
>>
>>
>
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