From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jul 23 2018 - 16:10:50 CDT
Please keep the list CC'ed on the replies.
The best solution for performance will depend on the system size and the
number of atoms involved. Without knowing the specifics, I wonder if NAMD
is the most appropriate software for this simulation.
Jerome
On Sun, 22 Jul 2018 at 15:54, Abhijit Gogoi <gogoiabhijit10_at_gmail.com>
wrote:
> Dear Jerome,
> Thanks for your reply. I want to constrain each
> atom individually, but with SMD it is not possible. As I mentioned earlier
> I have two different parts in my system to constrain. For one part I have
> to apply constrain in all directions (XYZ) and for the other part I have to
> apply constrain only in XY plane.
>
> sincerely
> Abhijit Gogoi
>
> On Sat, Jul 21, 2018 at 4:36 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> Dear Abhijit,
>>
>> Do you want to constrain (or restrain) each atom individually, or the
>> center of mass of groups of atoms? In the second case, your most flexible
>> choice is Colvars (
>> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html),
>> using the *distance* and *distanceXY* coordinates.
>>
>> Best,
>> Jerome
>>
>> On Fri, 20 Jul 2018 at 08:18, Abhijit Gogoi <gogoiabhijit10_at_gmail.com>
>> wrote:
>>
>>> Dear All,
>>> I want to constrain 2 parts of my simulation system. For
>>> one part I want to apply constrain in all (X,Y,Z) directions and for the
>>> other part I want to apply constrain only is XY plane. Is it possible with
>>> "constraints" option of NAMD.
>>>
>>> I have tried "constraints" option for one part for constraining all the
>>> directions and for constraining the other part in XY plane I have used
>>> "SMD". However with SMD only center of mass will be constrained, but I want
>>> to constrain each atom of that part.
>>>
>>> Please suggest something.
>>>
>>> sincerely
>>> Abhijit Gogoi
>>>
>>
>
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