From: Shaon Chakrabarti (shaonc_at_gmail.com)
Date: Wed May 23 2012 - 17:11:13 CDT
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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