# Re: Issues with 'Gyration' in Colvars module

From: Shaon Chakrabarti (shaonc_at_gmail.com)
Date: Wed May 23 2012 - 17:25:09 CDT

...And here are the details of 1)

The following calculations have been
done on a pdb file (which I could send
separately) grabbed from the end of
a trajectory run. The psf file I used in
VMD is the same one I used to run
the NAMD simulation.

MY CALCULATION: (x,y,z denote atom coordinates)
a) Rg defined with center of mass:
Rg = sqrt[1/N * sum over all N atoms{(x-COMx)^2+(y-COMy)^2+(z-COMz)^2} ]

With this definition I get Rg = 5.7555

b) Rg defined with center of geometry:
COGx = (1/N * sum of all x components). Similarly for COGy, COGz
Rg = sqrt[1/N * sum over all N atoms{(x-COGx)^2+(y-COGy)^2+(z-COGz)^2}
]

With this definition I get Rg = 5.754163

VMD MEASURE RGYR:
this gives Rg = 5.7541623 --almost identical to the result of part b)
above

COLVARS OUTPUT (from colvars.traj file):
this gives Rg = 5.579920

Hope this helps...

Thanks,
Shaon

On Wed, May 23, 2012 at 3:11 PM, Shaon Chakrabarti <shaonc_at_gmail.com> wrote:

> Hi Aron and Giacomo,
> Thanks a lot for such quick replies! Actually I had
> already done what Aron suggested: I first ran a 6ns
> long equilibration trajectory without the ABF module,
> but with gyration on.
> From the last parts of this trajectory, I created pdb
> and psf files of the molecule with Rg within the
> required range. Then I reinitialized the velocities and
> ran the trajectory with ABF included. I'm attaching the
> initial bit of colvars.traj file here--the range is 7-11 (i had the
> file for this range). The starting Rg value is about 8...
> so that is between 7 and 11...yet, the Rg value doesn't
> stay within the required range!
> I'm also attaching the colvars configuration file if that helps.
>
> About 1) ...I will provide the numbers and details of my code in
> a little while.
>
> Thanks again for all the help,
>
> Shaon
>
>
>
>
>
>
>
> On Wed, May 23, 2012 at 1:27 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
>
>>
>> About 1), can you provide the exact numbers, and more details regarding
>> your own calculation? Do you load the same PSF topology and coordinates in
>> VMD or use the masses guessed by VMD?
>>
>> In the colvars module, gyration is computed as the mass-weighted square
>> distance from the center of geometry, taken under square root. But I
>> actually realize now that the formula in the user's guide:
>>
>> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION0001322170000000000000
>> does not include the weighting masses. Would that explain the small
>> difference that you saw? If so, I apologize for the omission of the masses
>> in the user's guide.
>>
>> The gyration defined in VMD is also mass-weighted, but uses the center of
>> mass.
>>
>> In gyration, it seems contradictory to have mass-weighted gyration around
>> the center of geometry and not mass, but we decided towards that considered
>> that gyration can be and is often used in combination with RMSD.
>>
>> On Wed, May 23, 2012 at 3:56 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>>
>>> Hi Shaon,
>>>
>>> I've no idea about 1), but for 2), what happens if you specifiy Rg to be
>>> within 4-7 rather than 5-7? From my understanding the ABF method needs to
>>> sample forces before it starts to apply a bias, so if you're system starts
>>> outside the biasing range, it will never collect any samples, and hence
>>> never start to apply a bias. That would be my first thought anyway. If
>>> you really want to do 5-7 angstroms, you should apply a harmonic potential
>>> on Rg and sit it ~6 angstroms in order to equilibrate the system before
>>> running ABF.
>>>
>>> ~Aron
>>>
>>>
>>> On Wed, May 23, 2012 at 3:48 PM, Shaon Chakrabarti <shaonc_at_gmail.com>wrote:
>>>
>>>> Hi NAMD experts,
>>>> I'm facing two problems with the gyration component in
>>>> the Colvars module.
>>>>
>>>> 1) The NAMD user's guide says that the radius of gyration
>>>> is defined using the Center of Geometry. However, when
>>>> I write my own code (using the COG definition) to compute
>>>> the Rg of a molecule, the Rg value is always about 0.2
>>>> angstroms more compared to the output in the 'colvars.traj'
>>>> file. The values from my code exactly match the values
>>>> I get if I use the 'measure rgyr' command in VMD. I also
>>>> computed Rg using Center of Mass, but that makes the
>>>> difference even larger. I'd be grateful if someone can tell
>>>> me if I'm making a mistake somewhere, or if Rg is
>>>> actually defined differently in the Colvars module.
>>>> P.S. My molecule (about 30 angstroms long when fully
>>>> extended) is in the middle of a water box of side 55
>>>> angstroms.
>>>>
>>>>
>>>>
>>>> 2) The second problem is similar (as I understand from
>>>> the threads in 2008) to what Subramanian
>>>> Vaitheeswaran faced while using the gyration
>>>> component with ABF. If I specify the Rg to be (say)
>>>> within say 5 and 7 angstroms, and use ABF to get
>>>> the PMF, the system hovers at Rg value around
>>>> 4.5-4.8 most of the time! A final resolution doesn't
>>>> seem to have been posted back in 2008, and it
>>>> would be of immense help if someone could tell
>>>> me what's going on....if the problem has been
>>>> resolved. I tried switching the hideJacobian option
>>>> to yes, and increasing the lower and upper wall
>>>> constants, but these don't make any difference.
>>>>
>>>>
>>>> It would be great if someone could help with these two issues.
>>>>
>>>> Thanks,
>>>> Shaon
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>>
>>
>

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