From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Apr 10 2006 - 09:52:05 CDT
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
------------------------------------------------------------
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