Re: Error in PMF Calculations

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Fri Apr 05 2019 - 08:42:08 CDT

“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

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