Dear Lloyd, I have read that but my system is different
regards, On Thu, May 30, 2013 at 8:28 PM, lloyd riggs <lloyd.ri...@gmx.ch> wrote: > Dear Jiom, > > Look at justines tutorial, there's example pull .mdp. > > Stephan Watkins > > *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr > *Von:* "gromacs query" <gromacsqu...@gmail.com> > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org> > *Betreff:* [gmx-users] umbrella sampling for two polymer interaction > Dear All, > > I want to do Umbrella sampling between two different polymers (A and B) > interacting with each other with starting configuration separated by some > distance and I am trying to bring them closer. > > I have some queries regarding pull inputs: (this is for to run a umbrella > sampling at some distance) > > pull = umbrella > pull_geometry = distance > pull_dim = Y Y Y > pull_start = ??? > pull_ngroups = 2? > pull_group0 = polymer_B > pull_group1 = polymer_A > pull_init1 = 0 > pull_rate1 = 0.0 > > > please suggest for following: > > 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make > it interact with some directional vector > > 2) Which should be group0 or group1, in other words should I pull both > together or how I should decide which one should be reference and > which to be pulled as both are different polymers? > > 3) And also what should be pull_ngroups because if there is no > reference group then it should be 2 > > 4) I am not able to understand pull_start option with pull_init1. In > this case if it is set to yes and 0.0 respectively then does that mean > this combination is equivalent to pull_start = No if I just assume > pull_init1 does not have any default value (which is 0.0); not > existing > > 5) Also finally where are upper and lower bounds defined. pull_k1 = > 1000 is harmonic applied to some equilibrium distance value. How this > distance is taken by the programme (or it is just the starting > distance taken between two groups) and what are the +/- values > defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is > assumed equilibrium value and r1 is lower and r4 is upper value which > defines shape of potential) > > > thanks, > > Jiom > -- > 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 > > -- > 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 > -- 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
