Re: How to "twist" a molecule? (resubmit)

From: Margaret S. Cheung (mscheung_at_UH.EDU)
Date: Mon Jun 11 2007 - 17:49:57 CDT

Hi All,

I think I will need to revisit this problem, because I just realized
that NAMD program is not rotating the molecule even though the
configuration file was set so.

My configuration file

rotConstraints on
rotConsAxis x y z
rotConsPivot x y z
rotConsVel xx

But in the log file, it gave me warning as

Warning: The following variables were set in the configuration file but
were not needed.
Warning: rotConstraints
....

And I tried to see if rotConsPivot is in the log file, and they are not!
Does it mean that my NAMD program is not rotating the molecule?

Please help!
Sincerely,
Margaret

Grzegorz Jezierski wrote:
> Dear Margaret,
> Now I think I understand your problem.
> As mentioned on p.71 of NAMD manual, Rotating Constraints are set up
> the way ordinary (i.e. positional) restraints are.
> In my example, reference positions for Rotating Constraints are
> specified in R6G_6CAA.pdb file, and force constants are specified in
> fixed.pdb file, in 10th column.
> A line in my fixed.pdb file which specifies the force constant for
> Rotating Constraints looks like this:
> ATOM 46 O1 MOL 2 -0.300 -1.495 2.119 0.00 1.00
> If I put e.g. 0.00 instead of 1.00, the Rotating Constraints option
> for this atom will be switched off.
> Now in order to combine his with harmonic restraints, include your
> desired restraint definition in a separate file (pmf.conf in my
> example); description on p.82, use 'mcti' keyword. Specify
> 'freeEnergy on'. I used this option for constraining a system, not
> just for free energy calculations.
> Alternatively, you may want to specify 'fixed atoms'. This seems like
> a more suitable option for your study. In this case, you should use a
> different column (e.g. 'O' i.e. 9th) in the pdb file.
> Hope this helps
>
> Margaret S. Cheung wrote:
>> Hello,
>>
>> I tried with both rotational and harmonic contraints, but now I see
>> the possible problem JC mentioned.
>>
>> The question is "how to set reference positions for rotating
>> constraints"? The manual simply said that the rotational constraints
>> parameters are specified in the same manner as for usual
>> (static)harmonic constraints". I assume it means that we need to set
>> consref, conskfile, conskcol for the harmonic constraints.
>>
>> But if I now included rotational constraints to harmonic one, how can
>> I set the reference positions for rotation since all it has is
>> rotConsAxis, rotConsPivot and rotConsVel?
>> When I set constraints on, did it mean "all atoms" in the system will
>> be rotated? Can I apply rotation (twist) to only a part of the
>> molecules (e.g. excluding water molecules)?
>> Thank you.
>> Sincerely,
>> Margaret
>>
>> Grzegorz Jezierski wrote:
>>> I've run simulations with almost any combination of Rotating
>>> Constraints, Harmonic Constraints, Fixed Atoms and PMF constraints.
>>> Here is a relevant part of one of my input files:
>>>
>>> Constraints on
>>> consRef R6G_6CAA.pdb
>>> consKFile fixed.pdb
>>> consKCol B
>>>
>>> rotConstraints on
>>> rotConsAxis 3.50 4.15 -20.45
>>> rotConsPivot 3.50 4.15 -24.37
>>> rotConsVel 0.0030
>>> freeEnergy on
>>> freeEnergyConfig pmf.conf
>>>
>>>
>>> Regards,
>>> Greg
>>>
>>>
>>> On Sun, 25 Mar 2007, JC Gumbart wrote:
>>>
>>>
>>>> Your suggestion definitely sounds like it might work (using
>>>> fixedAtoms that
>>>> is); you can't use harmonic constraints and rotating constraints at
>>>> the same
>>>> time though, if I understand the manual correctly. I haven't seen
>>>> rotatingConstraints used by anyone myself, so you may just need to
>>>> experiment
>>>> with it. You could also try using IMD to control the forces
>>>> interactively.
>>>> Let us know how it goes.
>>>>
>>>>
>>>> On Mar 23, 2007, at 11:05 AM, Margaret S. Cheung wrote:
>>>>
>>>>
>>>>> (I apologize if you are reading this message again. The previous
>>>>> one perhaps
>>>>> was
>>>>> bounced because I haven't registered my current email address to
>>>>> NAMD-L, as
>>>>> warned
>>>>> by NAMD-L regulators)
>>>>>
>>>>> Hi NAMD users and developers,
>>>>>
>>>>> I'd like to "twist" a molecule by applying a torque along an axis.
>>>>> I am
>>>>> looking at "rotating constraints" in the user guide. But a simple
>>>>> rotation
>>>>> is not what I want. Somehow I would want to "fix" a few distant
>>>>> atoms away
>>>>> from the pivot point so that the molecules can be twisted
>>>>> eventually (ex:
>>>>> like winding up a helical structure). If so, would you recommend
>>>>> including
>>>>> "harmonic constraints" or simply assigning a few "fixed" atoms to the
>>>>> reference pdb file in order to accomplish that? Please advise and
>>>>> thank you
>>>>> for your time.
>>>>>
>>>>> Margaret S. Cheung
>>>>> Assistant Professor
>>>>> Department of Physics
>>>>> 629C Science and Research 1
>>>>> University of Houston
>>>>> Houston, TX 77204-5005
>>>>> email: mscheung_at_uh.edu
>>>>> (O)713-743-8358 (F)713-743-3589
>>>>> http://thoth.phys.uh.edu/~mscheung/
>>>>>
>>>>
>>>
>>>
>>
>
>

-- 
Margaret S. Cheung
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
email:   mscheung_at_uh.edu
(O)713-743-8358 (F)713-743-3589
http://thoth.phys.uh.edu/~mscheung/

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