Metadynamics with NWChem
Just Got Here
2:19:01 AM PST - Sat, Jan 14th 2017
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

  1. (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.

Just Got Here
8:41:32 AM PST - Mon, Feb 18th 2019
Metadynamics free energy calculation
Hello,

I have the same problem. I ran the NWChem Metadynamics tutorial example 1. I'm trying to generate the free energy plot from the Metadynamics result. I have a doubt which output file contains the free energy results.

I'm guessing xx.meta_gaussian file might contain the potential energy, but could not figure it out the meaning of each column: E(2)-E(31)+E(32), E(3), E(4), E(31), E(32).


Thank you very much in advance.


Best,
Eunbyeol

Gets Around
10:54:55 AM PDT - Fri, May 24th 2019
Please respond to these queries
These posts have been read over 1200 times, which indicates a lot of interest from the community in using NWChem for metadynamics calculations. The posts raise legitimate questions, especially, how does one extract the free energy change from the output?

Just Got Here
12:55:43 PM PST - Mon, Jan 13th 2020
Wrong geometry conversion when running metadynamics for periodic system
Hi Nwchem users and developers

I am having issues with running metadynamics calculation due wrong geometry conversion for angstrom to a.u. Below are the input and output geometry after conversion.

      1. input geometry

geometry units angstrom nocenter noautosym noautoz print xyz
O 1.8721262729142700 2.6772977892108072 3.0457634041233832
H 1.8721262729142700 3.4405367892108294 2.4494544041234025 mass 2.0
H 1.8721262729142700 1.9140587892107965 2.4494544041234025 mass 2.0
O 3.0007245151628497 1.6057278693301698 1.2975208145820827
H 3.0007245151628497 2.3689668693301926 0.7012118145821018 mass 2.0
H 3.0007245151628497 0.8424888693301587 0.7012118145821018 mass 2.0
end

  1. set nwpw:cif_filename neptunium4

nwpw
 np_dimensions -1 4

 xc xperdew91

 simulation_cell units angstroms

  boundary_conditions periodic

  lattice

   lat_a 3.91

   lat_b 3.91

   lat_c 3.91

  end

    1. Output geometry after conversion to AU

atomic composition:
    O   :  2     H   :  4



initial position of ions:

       1 O    (    3.53781   -2.32947   -1.63317 ) - atomic mass=  15.995

       2 H    (    3.53781   -0.88716   -2.76003 ) - atomic mass=   2.000

       3 H    (    3.53781    3.61705   -2.76003 ) - atomic mass=   2.000

       4 O    (   -1.71828    3.03439    2.45196 ) - atomic mass=  15.995

       5 H    (   -1.71828   -2.91213    1.32510 ) - atomic mass=   2.000

       6 H    (   -1.71828    1.59207    1.32510 ) - atomic mass=   2.000


    1. The right geometry output after conversion

O 3.53781 5.05936 5.755659
H 3.53781 6.50167 4.628799
H 3.53781 3.61705 4.628799
O 5.67055 3.03439 2.451960
H 5.67055 4.47669 1.325100
H 5.67055 1.59207 1.325100


The wrong geometry conversion causes error in the metadynamics calculations because the metadynamics calculation is done with a wrong geometry. Please I need help with fixing the error.


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