Re: Error in PMF Calculations

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Wed Apr 10 2019 - 02:02:20 CDT

 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

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