[CP2K-user] [CP2K:20374] Re: unable to analyse the metadynamics output file of the cp2k

['Karl Irikura' via cp2k]

Thanks, David, the "graph" program is working for me.

What are the energy units in the file "fes.dat"?  The well depths are < 0.1 
units.  

More generally, is it better to run one series of simulations for each 
collective variable, or a single series with two collective variables?  In 
my case there are two titratable groups and I'm trying to calculate pKa. 

Thanks,
Karl

On Thursday, May 9, 2024 at 6:02:27 AM UTC-4 David M. Sherman wrote:

> You're right: the tutorials don't see to explain this bit at all...
>
> You need to use the "graph" program which comes with cp2k. When you do a 
> metadynamics run, the resulting *.restart file will contain a record of all 
> of the HILLS  added during the metadynamics simulation. Note that if you do 
> a multiple-walker run, the *.restart file in any one of the walker 
> directories will also have all the hills from all the other walkers. Let's 
> assume you did a metadynamics simulation with 2 COLVARS and this generated 
> a restart file named "mysim.restart".  To turn that record of HILLS in the 
> restart file into a one-dimensional free-energy surface with respect to the 
> first COLVAR, you run the program graph.psmp using the following syntax:
>
> graph.psmp -cp2k -ndim 2 -ndw 1 -file mysim.restart
>
> If you want  a one-dimensional free energy surface with respect to the 
> second COLVAR, you run
>
> graph.psmp -cp2k -ndim 2 -ndw 2  -file mysim.restart
>
> (Note: BE VERY CAREFUL HERE!  Even though you only want a one dimensional 
> fes, the argument to -ndim MUST be the actual number of COLVARS that were 
> used in the metadynamics run.  The argument to -ndw is which COLVAR(S) you 
> want to generate the free-energy surface with respect to.  If you 
> accidently use -ndim 1, you will get what looks like a perfectly sensible 
> fes, but it will be completely erroneous).
>
> Running the graph program will generate a file called fes.dat that you can 
> plot with gnuplot to see the free energy surface.  Here's an example of a 
> gnuplot script to
> generate the plot (note: I'm converting my Cl coordination number COLVAR 
> into a sensible number by multiplying it by the number of Cl atoms in the 
> cell  and converting the free energy from AU to kJ/mole).
>
> set xlabel "Cl CN"
> #set terminal svg
> set xrange[-1:4]
> set yrange[-230:-120]
> plot "fes.dat" using ($1*4):($2*2625.5) with lines
> pause -1 "Hit any key to continue"
>
> Now,  if you want a 2-dimensional plot of the the free energy surface 
> (i.e., over both
> COLVARS) then you run:
>
> graph.psmp -cp2k -ndim 2 -ndw 1 2 -file mysim.restart
>
> and plot that using gnuplot.  Here's a gnuplot input script to generate a 
> contour map:
>
> set view map
> unset surface
> set contour
> set cntrparam levels 30
> set dgrid3d 100,100,1
> set xlabel "Cl CN"
> set ylabel "O CN"
> set style line 1 lc rgb "black" lw 1
> set style increment user
> #set terminal svg
> splot [-1:4] [-1:5] "fes.dat" using ($1*4.):($2*55):($3*2625.5) with lines
> pause -1 "Hit any key to continue"
>
> Have fun!
>
> On Tuesday, May 7, 2024 at 10:33:31 PM UTC+1 Karl Irikura wrote:
>
>> I have the same question.  That tutorial does not explain how to extract 
>> free energy information from the output files.  
>>
>> Thanks for any tips,
>> Karl
>>
>> On Thursday, January 11, 2024 at 7:52:20 AM UTC-5 Marcella Iannuzzi wrote:
>>
>>> Please refer to some tutorial like
>>> https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1
>>>
>>> Regards
>>> Marcella
>>>
>>>
>>> On Wednesday, January 10, 2024 at 1:02:01 PM UTC+1 cy22res... at iith.ac.in 
>>> wrote:
>>>
>>>> Hey Good afternoon everyone
>>>> Can anybody known how to analysis the cp2k metadynamics file? Please 
>>>> help if possible
>>>> Thank you
>>>> Deewan
>>>>
>>>

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