# RE: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Apr 10 2006 - 12:54:57 CDT

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 with your
> thoughts.
> 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 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
>> ------------------------------------------------------------
>>
>>
>
> 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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