Re:

From: Abhijit Gogoi (gogoiabhijit10_at_gmail.com)
Date: Mon Jul 23 2018 - 22:54:06 CDT

Dear Fiorin,
                   Thanks a lot for your suggestion. I can go for
fixedAtoms option for atoms that do not move at all. However, if I fixed
all those atoms (which do not move) how it will affect my simulations ? I
guess in that case those atoms (which are fixed) will not have any
interactions with the surrounding atoms. I can go for
*fixedAtomsForces *option.
But in this link (http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html)
as suggested "This option is required to turn fixed atoms off in the middle
of a simulation. These forces will affect the pressure calculation, and you
should leave this option off when using constant pressure if the
coordinates of the fixed atoms have not been minimized. The use of constant
pressure with significant numbers of fixed atoms is not recommended."

I would be grateful if you please clarify this point.

Sincerely
Abhijit Gogoi

On Mon, Jul 23, 2018 at 10:09 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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