Thanks, David, the "graph" program is working for me.<div><br /></div><div>What are the energy units in the file "fes.dat"? The well depths are < 0.1 units. </div><div><br /></div><div>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. </div><div><br /></div><div>Thanks,</div><div>Karl<br /><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, May 9, 2024 at 6:02:27 AM UTC-4 David M. Sherman wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>You're right: the tutorials don't see to explain this bit at all...</div><div><br></div><div>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:</div><div><br></div><div>graph.psmp -cp2k -ndim 2 -ndw 1 -file mysim.restart</div><div><br></div><div>If you want a one-dimensional free energy surface with respect to the second COLVAR, you run</div><div><br></div><div>graph.psmp -cp2k -ndim 2 -ndw 2 -file mysim.restart<br></div><div><br></div><div>(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).</div><div><br></div><div>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</div><div>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).</div><div><br></div><div>set xlabel "Cl CN"<br>#set terminal svg<br>set xrange[-1:4]<br>set yrange[-230:-120]<br>plot "fes.dat" using ($1*4):($2*2625.5) with lines<br>pause -1 "Hit any key to continue"<br></div><div><br></div><div>Now, if you want a 2-dimensional plot of the the free energy surface (i.e., over both</div><div>COLVARS) then you run:</div><div><br></div><div>graph.psmp -cp2k -ndim 2 -ndw 1 2 -file mysim.restart</div><div><br></div><div>and plot that using gnuplot. Here's a gnuplot input script to generate a contour map:</div><div><br></div><div>set view map<br>unset surface<br>set contour<br>set cntrparam levels 30<br>set dgrid3d 100,100,1<br>set xlabel "Cl CN"<br>set ylabel "O CN"<br>set style line 1 lc rgb "black" lw 1<br>set style increment user<br>#set terminal svg<br>splot [-1:4] [-1:5] "fes.dat" using ($1*4.):($2*55):($3*2625.5) with lines<br>pause -1 "Hit any key to continue"<br></div><div><br></div><div>Have fun!</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, May 7, 2024 at 10:33:31 PM UTC+1 Karl Irikura wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I have the same question. That tutorial does not explain how to extract free energy information from the output files. <div><br></div><div>Thanks for any tips,</div><div>Karl<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, January 11, 2024 at 7:52:20 AM UTC-5 Marcella Iannuzzi wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Please refer to some tutorial like</div><div><a href="https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1&source=gmail&ust=1719076166468000&usg=AOvVaw1FqRus52XuFhj2oMe8Ma21">https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1</a><br></div><div><br></div><div>Regards</div><div>Marcella</div><br><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, January 10, 2024 at 1:02:01 PM UTC+1 <a rel="nofollow">cy22res...@iith.ac.in</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Hey Good afternoon everyone</div><div>Can anybody known how to analysis the cp2k metadynamics file? Please help if possible</div><div>Thank you</div><div>Deewan<br></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/c17d03cf-6e2e-4c67-8542-0339d414d490n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/c17d03cf-6e2e-4c67-8542-0339d414d490n%40googlegroups.com</a>.<br />