| 2:19:01 AM PST - Sat, Jan 14th 2017 |
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Hi NWChem users and developers
I have doing the metadynamics tutorial described in this pdf
http://nwchemgit.github.io/images/Nwchem-new-pmf.pdf
I have doubts about the meaning of some output files after the metadynamics calculations. For example, the exercise 1, the dissociation reaction CH3Cl ? CH3+ + Cl- .
There are 11 calls to do the metadynamic calculation by
“task pspw car-parrinello”
Every before task makes 20000 steps (loop 10 2000) doing a print every 1000 steps (print_shift 1). Therefore every task makes 20 prints times 11 calls, it generates 220 meta00xxx.dat files. These .dat files contain the bias potential for every 10 gaussians added.
Doubt: the meta000001.dat (first print file from first task) contains C-Cl distance (au) vs. bias potential after addition of 10 gaussians. File meta000220.dat (last print file from the 11th task) contains the bias potential after 2200 gaussians. Is it correct?
My next doubt is about the summary file created called CH3Cl.meta_gaussians.
This file contains 2200 row entries (I guess one for each added gaussian). The meaning of the first three columns is clear but I would need clarification about the remaining column labels:
E(2)-E(31)+E(32)
E(3)
E(4)
E(31)
E(32)
It seems that E(2) would be the potential gain of the system due to adding gaussians. E(31) would be the potential only due to the gaussians. Therefore E(2)-E(31)+E(32) would be the potential of the system after substract the gaussians (E(32) is always 0). It draws like a blurred equipotential line of the system vs the collective variable. Is it ok?
What is the meaning of E(3) and E(4)?.
In this specific example, what is the best way to extract height energy barrier, from the blurred line E(2)-E(31)+E(32) or from the meta000xxx.dat profiles above the 7th task?
I think that I found a little bug doing the example 2 of the tutorial. The example in this case is sampling 2 CV but the corresponding meta_gaussians file is using a row labeling the columns like this
- (r(i),i=1,n),(sigma(i),i=1,n),w,E(2)-E(31)+E(32),E(3),E(4),E(31),E(32)
However, the file contains the necessary information of the 2 Cvs.
Thank you very much in advance for your help.
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