From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu May 24 2012 - 09:01:09 CDT
Hello Shaon, I don't see the masses in your formula, what happens if you
include them? I have a feeling that the numbers would coincide in that
case.
On the other question, Aron wrote you already what would have been my
thoughts on the trajectory.
Giacomo
On Wed, May 23, 2012 at 6:25 PM, Shaon Chakrabarti <shaonc_at_gmail.com> wrote:
>
> ....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
>>>>
>>>>
>>>
>>
>
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