# Re: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Apr 10 2006 - 18:26:27 CDT

Dear JC and namd users,

That syntax was from the free energy perturbation calculation; I want to
have a group of atoms being constained at their center of mass...
I don't know if I am doing the right thing for the syntax...

I am only interested in applying forces in a local motif, but didn't
really want to have the rest of atoms being fixed or constrained at their
positions; I want to have the rest of atoms being constrained at their
center of mass... My protein is not elastic so I may not expect the rest
of the protein remains intact while I'm tearing off its motif.

Thanks.
Margaret

On Mon, 10 Apr 2006, JC Gumbart wrote:

> 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 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.
>>>>> Please share me with your insights!
>>>>> 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
>> ------------------------------------------------------------
>

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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