# Re: NAMD-L: question about harmonic constraints

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 10 2006 - 17:50:58 CDT

I'm not sure I follow completely...where did that syntax come up?

Also, could you explain why you want the forces that are applied to
group B also applied to group A? Any natural interaction between them
will be handled by NAMD, so I'm not sure why you want a reciprocal
force artificially applied.

Any clarification would be much appreciated.

On Apr 10, 2006, at 12:54 PM, Margaret Shun Cheung wrote:

>
> Dear JC and NAMD users,
> This is a follow-up of the question: how to put constaints on a
> center-of-mass of several residues (e.g. group A) to a specific
> coordinate (e.g. center of mass of group A: x,y,z) . Somehow this
> syntax comes up. Please take a look,
>
> urestraint{
> {posi group (segnameA,1) to (segnameA, 10)} kf=20 ref=(x, y, z)
> }
>
> Does it make sense if used with SMD on (e.g. group B)?
> Thank you very much.
> Sincerely,
> Margaret
>
> On Mon, 10 Apr 2006, Margaret Shun Cheung wrote:
>
>>
>> Dear JC and NAMD users,
>> Thanks for the info. I'd like to have a group of atoms (group A)
>> restrained to their center of mass while the other group of atoms
>> (group B) were pulled by SMD (so SMDatoms are taken). I looked up the
>> user guide and wonder if there is an option to include the
>> reciprocal forces of group B (the force being pulled at a constant
>> velocity, so it will change in each time step) as the input force for
>> group A defined in "addforce" (newtonian third law...).
>> From the user guide, it looks like there is only one fixed force
>> available
>> to addgroup; I don't know if it's true.
>>
>> I tried to avoid using "fixedatom" or "constraints" for each atom in
>> group A because my system is far from a rigid body.
>> Or is there some other way to get around with it, please share me
>> Thank you very much.
>> Sincerely,
>> Margaret
>>
>>
>> On Mon, 10 Apr 2006, 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
>>>> 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
>>> ------------------------------------------------------------
>>
>> 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
> ------------------------------------------------------------

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