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
