Re: Error in PMF Calculations

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Wed Apr 10 2019 - 03:38:22 CDT

" I am able to find the residue at distances in 3 < COM
(residue)-COM(sheet)<6 " how you calculated this?

On Wed, Apr 10, 2019 at 1:43 PM HEMANTH H 18310019 <hemanth.h_at_iitgn.ac.in>
wrote:

> Yes, I am able to find the residue at distances in 3 < COM
> (residue)-COM(sheet)<6. But the same count does not reflect in the *. count
> file
>
> On Wed 10 Apr, 2019, 1:37 PM Souvik Sinha, <souvik.sinha893_at_gmail.com>
> wrote:
>
>> Does it mean, in *.colvars.traj, your colvar values are greater than 6
>> (for the window 3-6 Ang)? If so, your boundary potentials are not able to
>> keep your molecule so close to the graphene sheet may be due to 'sterical
>> restriction' as Jeff mentioned earlier. Then what do you mean by this " At
>> the lowest point, I can find the molecules near to the surface of the
>> sheet"? Did you find ' 3 < COM(molecule) - COM(sheet) < 6 ' or some atom
>> of your bulk molecule randomly approaching surface but not the whole one?
>>
>> I am not sure but increasing boundary potentials may keep your molecule
>> in the nearest bin to the surface, however its significance is doubtful.
>>
>> On Wed, Apr 10, 2019 at 12:30 PM HEMANTH H 18310019 <
>> hemanth.h_at_iitgn.ac.in> wrote:
>>
>>> In the bins that correspond to the closest approach (3-6) the sampling
>>> is zero.
>>>
>>> On Wed 10 Apr, 2019, 12:19 PM Souvik Sinha, <souvik.sinha893_at_gmail.com>
>>> wrote:
>>>
>>>> In your closest bin/window to the graphene sheet, does the
>>>> colvar updates written in *.colvars.traj restricted within your defined
>>>> window upper and lower boundaries?
>>>>
>>>> Souvik
>>>>
>>>> On Wed, Apr 10, 2019 at 10:14 AM HEMANTH H 18310019 <
>>>> hemanth.h_at_iitgn.ac.in> wrote:
>>>>
>>>>> Sir,
>>>>>
>>>>> Yes, the system has multiple layers of graphene. I am following the
>>>>> tutorial that was available on your webpage for setting up the PMF
>>>>> calculations. I was using the same input script template, across different
>>>>> simulations, associated with different molecules.
>>>>>
>>>>> I have set the z-transition coordinate to be the distance between the
>>>>> centre of mass of the residue and that of the topmost graphene sheet.
>>>>>
>>>>> At the lowest point, I can find the molecules near to the surface of
>>>>> the sheet, but the same is not getting registered in the count files.
>>>>>
>>>>> Thanking you,
>>>>> Yours faithfully,
>>>>> Hemanth H
>>>>>
>>>>> On Fri, Apr 5, 2019 at 7:12 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:
>>>>>
>>>>>> “The sampling works for distances greater than 7 angstroms, and hence
>>>>>> the definition of transition coordinates must be right.”
>>>>>>
>>>>>> I don’t agree with this statement. I don’t think your transition
>>>>>> coordinate is defined how you are expecting.
>>>>>>
>>>>>> Do you have multiple layers of graphene? If the transition coordinate
>>>>>> is the center of mass of multiple layers, then you will not be able to
>>>>>> approach closely.
>>>>>>
>>>>>> What does system look like when the transition coordinate is at its
>>>>>> smallest value?
>>>>>>
>>>>>> Jeff
>>>>>>
>>>>>> On Thu, Apr 4, 2019 at 23:39 HEMANTH H 18310019 <
>>>>>> hemanth.h_at_iitgn.ac.in> wrote:
>>>>>>
>>>>>>> Sir,
>>>>>>>
>>>>>>> I'm using ABF to calculate the PMF for the adsorption of a Thymine
>>>>>>> residue. The sampling works for distances greater than 7 angstroms, and
>>>>>>> hence the definition of transition coordinates must be right. The sampling
>>>>>>> is zero in the region between 3-6 angstroms.
>>>>>>>
>>>>>>> On Thu, Apr 4, 2019 at 5:46 PM Jeff Comer <jeffcomer_at_gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Are you using ABF? At what distance from the sheet is the sampling
>>>>>>>> zero? How big is your molecule? What does the PMF look like?
>>>>>>>>
>>>>>>>> My guess is that you have big bulky molecule and it is sterically
>>>>>>>> restricted from approaching the sheet as closely as you think it should. If
>>>>>>>> so, this region of the transition coordinate is very high energy and not
>>>>>>>> relevant.
>>>>>>>>
>>>>>>>> Another possibility is that the definition of the transition
>>>>>>>> coordinate (in terms of atom serial numbers), is not what you think it is.
>>>>>>>>
>>>>>>>> Jeff
>>>>>>>>
>>>>>>>> On Thu, Apr 4, 2019 at 00:23 HEMANTH H 18310019 <
>>>>>>>> hemanth.h_at_iitgn.ac.in> wrote:
>>>>>>>>
>>>>>>>>> Dear all,
>>>>>>>>>
>>>>>>>>> I'm trying to calculate the PMF for the absorption of a molecule
>>>>>>>>> on a graphene sheet. The calculation is run for 100 ns, but the sampling in
>>>>>>>>> the region near the sheet is zero or very negligible even after running the
>>>>>>>>> simulation for an extended time ( ~200 ns). I also tried setting the window
>>>>>>>>> size to the region that was not being sampled, but that also didn't help.
>>>>>>>>> Any help in this regard would be highly appreciated.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> *Hemanth H 18310019*
>>>>>>>>> Research Scholar
>>>>>>>>> IIT Gandhinagar
>>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> –––––––––––––––––––––––––––––––––––———————
>>>>>>>> Jeffrey Comer, PhD
>>>>>>>> Assistant Professor
>>>>>>>> Institute of Computational Comparative Medicine
>>>>>>>> Nanotechnology Innovation Center of Kansas State
>>>>>>>> Kansas State University
>>>>>>>> Office: P-213 Mosier Hall
>>>>>>>> Phone: 785-532-6311
>>>>>>>> Website: http://jeffcomer.us
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> *Hemanth H 18310019*
>>>>>>> Research Scholar
>>>>>>> IIT Gandhinagar
>>>>>>>
>>>>>> --
>>>>>>
>>>>>> –––––––––––––––––––––––––––––––––––———————
>>>>>> Jeffrey Comer, PhD
>>>>>> Assistant Professor
>>>>>> Institute of Computational Comparative Medicine
>>>>>> Nanotechnology Innovation Center of Kansas State
>>>>>> Kansas State University
>>>>>> Office: P-213 Mosier Hall
>>>>>> Phone: 785-532-6311
>>>>>> Website: http://jeffcomer.us
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Hemanth H 18310019*
>>>>> Research Scholar
>>>>> IIT Gandhinagar
>>>>>
>>>>
>>>>
>>>> --
>>>> Souvik Sinha
>>>> Research Fellow
>>>> Bioinformatics Centre (SGD LAB)
>>>> Bose Institute
>>>>
>>>> Contact: 033 25693275
>>>>
>>>
>>
>> --
>> Souvik Sinha
>> Research Fellow
>> Bioinformatics Centre (SGD LAB)
>> Bose Institute
>>
>> Contact: 033 25693275
>>
>

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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