Re: restraining the COM of a group of atoms

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Sun Oct 11 2009 - 12:53:10 CDT

Thank you very much for all the suggestions.

Best,
Bin

On Oct 9, 2009, at 11:21 PM, Giacomo Fiorin wrote:

> Hi, indeed it's fairly easy with the collective variables module. You
> can define a "distance" colvar, where "group1" are the atoms of
> interest, and "group2" can be another group of atoms, or a dummy atom
> (keyword: dummyAtom) centered on the point of interest.
>
> The restraint can be applied in two ways: either by defining an
> upperWall to the colvar that can kicks in after a certain distance
> (including 0), or applying an harmonic bias centered in 0. The
> distance from the point of interest will be forced back to lower
> values, restraining the center of mass of the protein near there.
>
> Giacomo
>
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_at_gmail.com
> ---- ----
>
>
>
> On Fri, Oct 9, 2009 at 8:43 PM, Joshua Adelman
> <jadelman_at_berkeley.edu> wrote:
>> Hi Bin,
>>
>> This is pretty trivial to code up using the GlobalMasters routines
>> (at least
>> in v2.6). You'll have to write your own GlobalMaster code and
>> recompile
>> namd, but otherwise it's simple. Take a look at the
>> GlobalMasterMisc.C and
>> .h files in the src/ directory. This code will only run on the head
>> node,
>> but in my experience, unless you are doing something really
>> complicated, you
>> won't see any slowdown.
>>
>> If you want to see example code, let me know.
>>
>> Also, I haven't used the collective variable features in NAMD 2.7,
>> but
>> doesn't the "distance" collective variable basically allow you to
>> do this?
>>
>> Another alternative is to try PLUMED (which I have not):
>> http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
>>
>> Josh
>>
>>
>>
>>
>>
>> On Oct 9, 2009, at 8:19 PM, BIN ZHANG wrote:
>>
>>> Hi, All:
>>>
>>> Browsing through the mailing list, I saw quite a few people
>>> interested in
>>> restraining the center of mass (COM) of a group of atoms during
>>> their
>>> simulation. However, to my understanding, NAMD does not have an
>>> elegant way
>>> to do this (correct?). Though tclforces script could do the job,
>>> it would be
>>> a pain while the number of atoms is big.
>>>
>>> So my question is why does NAMD not offering this ability? It
>>> cannot be a
>>> coding issue. Actually, I think it's rather trivial to implement
>>> this, given
>>> that it already has SMD implemented. It should be basically the
>>> same as SMD,
>>> except here we have zero velocity, and also the moving direction
>>> is updated
>>> on the fly as r - r0.
>>>
>>> Am I missing something here? Is NAMD 2.7b1 already able to do
>>> this? If
>>> not, I would like to try to do it myself.
>>>
>>> Thanks for any comments.
>>>
>>> Best,
>>> Bin
>>>
>>
>>

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