**From:** Shaon Chakrabarti (*shaonc_at_gmail.com*)

**Date:** Wed May 23 2012 - 17:25:09 CDT

**Next message:**Aron Broom: "Re: Issues with 'Gyration' in Colvars module"**Previous message:**Shaon Chakrabarti: "Re: Issues with 'Gyration' in Colvars module"**In reply to:**Shaon Chakrabarti: "Re: Issues with 'Gyration' in Colvars module"**Next in thread:**Aron Broom: "Re: Issues with 'Gyration' in Colvars module"**Reply:**Aron Broom: "Re: Issues with 'Gyration' in Colvars module"**Reply:**Giacomo Fiorin: "Re: Issues with 'Gyration' in Colvars module"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

...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:
*

*>
*

*>> Hi Shaon, Aron has already answered well on 2).
*

*>>
*

*>> 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
*

*>>>
*

*>>>
*

*>>
*

*>
*

**Next message:**Aron Broom: "Re: Issues with 'Gyration' in Colvars module"**Previous message:**Shaon Chakrabarti: "Re: Issues with 'Gyration' in Colvars module"**In reply to:**Shaon Chakrabarti: "Re: Issues with 'Gyration' in Colvars module"**Next in thread:**Aron Broom: "Re: Issues with 'Gyration' in Colvars module"**Reply:**Aron Broom: "Re: Issues with 'Gyration' in Colvars module"**Reply:**Giacomo Fiorin: "Re: Issues with 'Gyration' in Colvars module"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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