Double wide sampling in free energy calculation

From NWChem

You are viewing a single post from the thread title above
Jump to: navigation, search

Click here for full thread
Clicked A Few Times
Threads 12
Posts 43
Hi,

I think there is a little error in the example of NWChem free energy calculation. Following is the input file of the example:

  md
system clfoh_neb
cutoff 1.5 qmmm 1.5
noshake solute
isotherm
end

  qmmm
print low
nsamples 1000
ncycles 2
end

  set qmmm:fep_geom clfoh_neb-s.xyzi clfoh_neb-e.xyzi
set qmmm:fep_esp clfoh_neb-s.esp clfoh_neb-e.esp
set qmmm:fep_lambda 0.0 0.1
set qmmm:fep_deriv .true.

  task qmmm dft fep

I am concerned is if set the double wide sampling, should we set fep_lambda as follows?

  set qmmm:fep_lambda 0.05 0.1
set qmmm:fep_deriv .true.

Two facts support my assumption. The one is NWChem manual tell us in the fep_lambda line we set λiandλi + 1, and also say

λi − 1 = λi − (λi + 1 − λi)

So if we set qmmm:fep_lambda 0.0 0.1, then λi − 1 = − 0.1. However we want to sample from 0.0 to 0.1, therefore I guess it should be 0.05 0.1.

Another reason is the computational results. I performed 3 calculations for the example with the following settings:

First:
  set qmmm:fep_lambda 0.0 0.1
#set qmmm:fep_deriv .true. # without using double wide sampling

Second:
 set qmmm:fep_lambda 0.0 0.1
set qmmm:fep_deriv .true.

Third:
 set qmmm:fep_lambda 0.05 0.1
set qmmm:fep_deriv .true.

The total free energy of first computation is 0.63 kcal/mol, agreement with the third result 0.68, but the second result is 1.74 kcal/mol.

Am I wrong? Any suggestion is appreciated.

I have another question here. While performing free energy calculation, NWChem generate .trj file frame by frame, can we change the writing frequency? Sometimes the .trj file is too large to treat. Thanks in advance.

Jingbo
Edited On 12:39:25 AM PST - Wed, Nov 27th 2013 by Wjb0920


Who's here now Members 0 Guests 0 Bots/Crawler 0


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC