Hello Justin I still don't understand where Gromacs takes the x coordinates in the output pmf with g_wham If I run g_wham with tpr-files and pullf-files without the pullx-files
-it tpr-files.dat -if pullf-files.dat I get a profile which means that g_wham does not take the X-coordinates in the pullx (I don't give them), but in the tpr files ... So what X-coordinates are stored in the tpr-files ? Then if I use -it tpr-files.dat -ix pullx-files.dat Where does g_wham take the forces and which x coordinates does it take : those from the tpr or those from the pullx ? Moreover when I restart my simulations, I regenerate new tpr files For instance to add 10 more ns gmx convert-tpr -s umbrella10ns.tpr -extend 10000 -o umbrella20ns.tpr gmx mdrun -s umbrella20ns.tpr -cpi xxx.cpt .... If I run g_wham after this simulation, which tpr should I use ? Can you please explain the role of these tpr in g_wham calculations? Thanks a lot On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote: > Hello Justin- > In MY pullx first column is Time and second column is absolute > coordinate of the COM of the pulled group Maybe we are missing an option > which would print X and dX in the pullx files - one of the pull-print stuffs > ???!!.. In that case too bad we would have tons of "bad" pull files Printing > the reaction coordinate (dX) should be the default .. Don't you think so ? > Hence my problem with wham using absolute coordinate instead of actual > distance between the two centers of mass What do you suggest to retrieve the > actual values of my reaction coordinate without rerrunning everything ? It should be straightforward to apply a systematic shift to the values in the output PMF curve. But I don't know how you've set up your pull code to get such output in the first place. The absolute position of group0 should be totally irrelevant. -Justin > Serge > > ************************* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
