Re: Error in PMF Calculations

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Thu Apr 04 2019 - 23:39:21 CDT

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--000000000000b259a50585c1120f--

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