Yeah I set pull_init =0, and pull_start = yes, and it still gave a "distance at start" as 0.78nm. It must be doing something funny because with pull_vec, because when I use pull_geometry = distance and pull_dim = Y Y Y, the distance 0.815nm is returned as the "distance at start", which is the actual distance between the two groups.
Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Sorry maybe I was unclear before with my first point; the specified >> distance in the mdp file is 0.78nm, which grompp returns back as the ref >> distance. The "distance at the start" that grompp returns is also >> 0.78nm, even though the actual distance is 0.815nm. That's why I was >> asking what this distance actually means, as it is not the absolute >> distance between the reference groups. > > As I said before, you're telling grompp to make that the reference > distance. You say "the specified distance in the mdp file is 0.78 nm," > therefore grompp is doing what it's told. If that's not the desired > distance, then don't set it as such. Have you tried the combination I > suggested in the last message? Does it give an initial distance of > 0.815 nm? > >> Also as regards to your second point; what if in the initial >> configurations the two reference groups do not lie along the stated >> vector? >> > > Hard to say, but probably you'll get some very high forces at the > outset of the simulation as the simulation as the umbrella potential > tries to force the pulled group to conform to the restraint > specifications. Whether or not that negatively impacts the ultimate > result of the simulation is also an important consideration. If > you're pulling along a given vector, you should start with your > reference coordinates as close to the desired location as possible. > > -Justin > >> Cheers >> >> Gavin >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> 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 ? >>>> >>> You're telling grompp that the initial distance is 0.78 nm, so it's >>> spitting that back out. If that's not the true distance, then specify >>> the correct quantity :) The distance should be correctly detected >>> with: >>> >>> pull_start = yes >>> pull_init = 0 >>> >>> As for the second question, the vector doesn't change over the >>> simulation, but the position of pull_group1 along that vector will. >>> That's what the umbrella potential is doing - it allows for harmonic >>> oscillation along any of the dimensions specified by pull_vec/pull_dim >>> (depending on the settings). >>> >>> -Justin >>> >> > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
