Hi Chris Seems my confusion was that I assumed that the distances in the profile.xvg-file should correspond to something I could measure with g_dist. Turns out it does not. Thank you for helping me sorting out this, I got it now :-)
About pull_pbcatom0 though. My box is >> 2*1.08 nm in all directions: $ tail -n 1 conf0.gro 12.45770 12.45770 17.99590 I am still not sure what pull_pbcatom0 does. You said it should not have any effect on my results, but changing it does result in a different initial distance reported by grompp. In my initial attempts at this, I did not specify anything for pull_pbcatom0, but in the grompp output I get this Pull group natoms pbc atom distance at start reference at t=0 0 21939 10970 1 1 0 2.083 2.083 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data Then, following the advice in the thread I referred to earlier, I set pull_pbcatom0 explicitly in the mdp-file to be an atom close to the COM of the Protein. Then I get from grompp Pull group natoms pbc atom distance at start reference at t=0 0 21939 7058 1 1 0 1.808 1.808 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data As you can see, the initial distance is different (2.083 vs 1.808), and 1.808 is the same as the distance reported by g_dist. Do you have any comments here as to why this is? Thanks /PK What you reported is not what you did. It appears that grompp, gtraj, and g_dist report the same value. Please also report the value that you get from your pullx.xvg file that you get from mdrun, which I suspect will also be the same. The difference that you report is actually between the first FRAME of your trajectory from g_dist and the first LINE of the file from the g_wham output. I see no reason to assume that the values in the output of g_wham must be time-ordered. Also, I have never used g_wham myself (I use an external program to do wham) and so I can not say if you are using it correctly. My overall conclusion is that you need to investigate g_wham output not worry about a new run at this stage. Regarding pull_pbcatom0, there is lots of information on the mailing list about this. It is a global atom number that defines the unit cell for selection of which periodic image of each molecule will be used for the pulling. If all of your box dimensions are >> 2*1.08 nm, then pull_pbcatom0 will not affect your results. Chris. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists