Re: Error in PMF Calculations

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Wed Apr 10 2019 - 01:59:53 CDT

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
>

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:37 CST