Re: Error in PMF Calculations

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Tue Apr 09 2019 - 23:42:20 CDT

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

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