Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus was 0.815 nm, which agreed with the distance I calculated using a molecular configuration editor. My question is therefore this, when using pull_geometry =direction with a specified vector, How should one interpret the initial distance provided by grompp? and how does Gromacs deal with the fact that the vector between the two point changes during the run ?
Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Many thanks for the reply I know technically I am doing two different >> things. However due to my starting conifgurations in both cases I would >> expect similar results. >> Could you confirm the following points >> >> 1) In pull_geometry=distance, and pull_dim =YYY; is the absolute >> distance between the COM of both groups in all directions considered ? >> > > Yes. > >> 2) In pull_geometry = direction, with a specified vector; I assume that >> it is the distance between the two groups along this vector that is >> considered? >> > > Should be. Compare the output of g_dist with what grompp reports as > the initial distance. > >> 3) Is the specified vector taken to be the vector connecting the two >> points? Therefore are the desired distances in the mdp files essentially >> the magnitudes of this vector at each window. >> > > Per the documentation, grompp normalizes the vector, so no, not > directly. But if you have proper settings for pull_init/pull_start, > then the reference distance should be correctly calculated along the > specified vector for each window. > > -Justin > -- 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