Hey, I appear to have serious trouble understanding how to set up the pulling properly.
I have many configurations of a protein partially adsorbed to a froozen surface (the configs differ in the amount of the protein that has been desorbed). Now I want the pulling to keep the distance of the desorbed end of the protein to the surface using the harmonic pot. Now the documentation is not very clear how this all works so I ran several experiments to figure it out but I failed. I use the following options: ;PULLING pull = umbrella pull_geometry = distance pull_dim = N N Y pull_nstxout = 1000 pull_nstfout = 1000 pull_ngroups = 1 pull_group0 = GLD pull_group1 = ASN pull_vec1 = 0.0 0.0 0.0 pull_init1 = 5.27778 pull_rate1 = 0.0 pull_k1 = 100 where gld is the surface and asn is the end residue of the protein and pull_init1 is set to the desired COM distance of the two groups (gld is froozen). I use the same settings for all runs, only changing pull_init1 to get the desired distance. Now for some reason using this setup either pulls the ASN end of the protein completely onto the surface or very far away from it depending on the value I use for pull_init1. So the distance between what and what shall I put for pull_init1? What else is wrong? Thx, Alex _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
