From NWChem
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Posts 43
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| 12:27:56 AM PST - Wed, Nov 27th 2013 |
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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
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Edited On 12:39:25 AM PST - Wed, Nov 27th 2013 by Wjb0920
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Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Threads 2
Posts 43
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| 9:19:56 PM PST - Fri, Dec 6th 2013 |
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You are right about double wide sampling. I must have typed it wrong in the example.
I have to look if I hard wired the writing frequency for the trajectory file or it can be changed at the input level. For now you can just keep the nsamples small and increase number of cycles.
Marat
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Clicked A Few Times
Threads 12
Posts 43
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| 11:37:12 PM PST - Wed, Dec 18th 2013 |
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thanks
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Quote:Marat Dec 7th 4:19 amYou are right about double wide sampling. I must have typed it wrong in the example.
I have to look if I hard wired the writing frequency for the trajectory file or it can be changed at the input level. For now you can just keep the nsamples small and increase number of cycles.
Marat
thank you very much! Marat.
I will follow your instructions to change the nsamples and ncycles. 
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