Re:

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jul 23 2018 - 17:09:14 CDT

Hello Abhijit, take a look at the NAMD manual under "Position restraints
parameters". You can choose individual Cartesian components (default: all,
or XYZ) to confine the X and Y coordinates of one group. For the atoms
that don't move at all, why not use fixedAtoms?

Note also that due to the traditional confusion of terms between holonomic
constraints (i.e. frozen coordinates) and harmonic restraints, and the fact
that you mentioned SMD along the way, most people here understood your
request as the latter. Please clarify it not the case.

Giacomo

On Mon, Jul 23, 2018 at 5:12 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__colvars.github.io_colvars-2Drefman-2Dnamd_colvars-2Drefman-2Dnamd.html&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=H8H8YfhjOICOv55h4aLvwMDTSsPZw9JrlBFJNEwdaX4&s=_z9RBGB2FFz_MyPCMGmk6JUho9nRhoHBc_vhBVq_Ysw&e=>),
>>> 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
>>>>
>>>
>>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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