# Re: NAMD-L: question about harmonic constraints

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 10 2006 - 17:21:27 CDT

The magnitude of the force is divided by total mass and then applied to
all atoms weighted by their mass. The direction of the force will be
the same for every atom though.

In other words, say you want to apply a force F = M*a to a group of
atoms (m1 + m2+...+mf = M). Then what tclforces will do is apply a
force f = mn*a to each atom n. The sum of the forces
m1*a+m2*a+...+mf*a = M*a is again the total force F.

I hope this makes sense...

On Apr 10, 2006, at 12:29 PM, Ioana Cozmuta wrote:

> this is an interesting topic.
>
> Pulling the center of the mass of a molecule implies that the atoms
> ahead of the center of mass are pushed while actually only the atoms
> following the center of mass are pulled. I am wondering what you mean
> exactly by "distributing the forces to each atom appropriately"?
> Does this imply that it takes care for all the atoms to be pulled?
>
> Ioana
>
>
> JC Gumbart wrote:
>> I'm almost positive that forces applied to the group are applied to
>> the
>> center of mass, which has to then be distributed to each atom
>> appropriately,
>> so it should be okay for your purpose.
>>
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>> Behalf
>> Of Margaret Shun Cheung
>> Sent: Saturday, April 08, 2006 10:30 PM
>> To: JC Gumbart
>> Cc: namd-l_at_ks.uiuc.edu
>> Subject: RE: namd-l: NAMD-L: question about harmonic constraints
>>
>>
>> Dear JC and NAMD users,
>> Thank you for the info. I checked tclForces on the manual and saw the
>> option of "addgroup". I am confused with its description
>> "...Aggregate forces may then be applied to the group as whole."..
>>
>> Assuming that my system is not a rigid body, I wonder whether the
>> description refers to the force acting to the center of mass or
>> acting to each atom in the group.
>> Thank you very much.
>> Sincerely,
>> Margaret
>>
>>
>> On Sat, 8 Apr 2006, JC Gumbart wrote:
>>
>>
>>> It is possible to use SMD with a velocity of zero to restrain the
>>> center
>>>
>> of
>>
>>> mass of atoms along one axis. However, if you try to restrain along
>>> more
>>> than one axis, very interesting problems will arise.
>>>
>>> Unfortunately, for anything more, I believe scripting with tclForces
>>> may
>>>
>> be
>>
>>> the only option.
>>>
>>> -----Original Message-----
>>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>>> Behalf
>>> Of Margaret Shun Cheung
>>> Sent: Saturday, April 08, 2006 1:34 PM
>>> To: namd-l_at_ks.uiuc.edu
>>> Subject: namd-l: NAMD-L: question about harmonic constraints
>>>
>>> Dear NAMD users,
>>>
>>> I looked up the user guide for harmonic constraints and the option
>>> is that
>>> each assigned atom is referenced to a specific coordinate in the
>>> "consref <file>". What should I do if I want to impose harmonic
>>> constraints to
>>> the center of mass of several atoms during the simulations instead
>>> (like
>>> what SMD does to the selected SMD atoms)? I looked up
>>> selectcontrX{Y,Z}
>>> too, but probably it's not what I was thinking for.
>>>
>>> Thank you very much!
>>> Sincerely,
>>> Margaret S. Cheung,
>>> Ph. D. Postdoctoral Fellow,
>>>
>>> ------------------------------------------------------------
>>> Room 2117 Tel: (301) 405-4892
>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>> University of Maryland http://glue.umd.edu/~mscheung
>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>> ------------------------------------------------------------
>>>
>>>
>>>
>>
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>>
>>
>>
>>
>
> --
> Ioana Cozmuta, Ph.D
> Eloret Corporation
> NASA Ames Research Center
> Mail Stop 230-3
> Moffett Field, CA 94035
> phone (650) 604-0993
> e-mail: icozmuta_at_mail.arc.nasa.gov
> http://people.nas.nasa.gov/~ioana/

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