Re: NAMD-L: question about harmonic constraints

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Apr 11 2006 - 17:41:08 CDT

The solution to your problem is to use SMD for one part and tcl forces
for the other.

For example, you can use SMD to restrain one part of the protein with
zero velocity along the axis of pulling (please remember, it can only
be one axis, x, y or z) and then use tcl forces to pull the other part
at constant velocity.

I've attached a script I used to pull a small deca-alanine helix in the
-z direction at constant velocity. I pulled the center of mass of the
10 C-alpha atoms. This along with the NAMD user guide section on
tclforces should give you a good start in using it for your purposes.


On Apr 10, 2006, at 6:26 PM, Margaret Shun Cheung wrote:

>
> 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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