**From:** HEMANTH H 18310019 (*hemanth.h_at_iitgn.ac.in*)

**Date:** Thu Apr 04 2019 - 23:39:21 CDT

**Next message:**Jeff Comer: "Re: Error in PMF Calculations"**Previous message:**Marcelo C. R. Melo: "Re: Pointcharge file in QM/MM setup with ORCA"**In reply to:**Jeff Comer: "Re: Error in PMF Calculations"**Next in thread:**Jeff Comer: "Re: Error in PMF Calculations"**Reply:**Jeff Comer: "Re: Error in PMF Calculations"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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--
*

**Next message:**Jeff Comer: "Re: Error in PMF Calculations"**Previous message:**Marcelo C. R. Melo: "Re: Pointcharge file in QM/MM setup with ORCA"**In reply to:**Jeff Comer: "Re: Error in PMF Calculations"**Next in thread:**Jeff Comer: "Re: Error in PMF Calculations"**Reply:**Jeff Comer: "Re: Error in PMF Calculations"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Sun Sep 15 2019 - 23:20:30 CDT
*