First of all it's best to post the error-message (i think there must be one). >From the pulling options below i would say the problem is probably that you >have 'pull_dim' and 'pull_geometry = direction', manual say 'pull_dim' is for >'distance' and 'position'. Another think is that you have in 'pull_vec1' 3 >dimensions and in 'pull_init1' only one, this could be the problem when you >used 'pull_geometry = position'. The last idea i have is this: 'pull_kB1 = >500'. The manual states that this is only for the free-energy-code. But this are only guesses, because we have no error-message and i have only used 'pull_dim = Y Y Y' with 'pull_geometry = position' (and that only once to try it out).
Below are the options which i used (GROMACS 4.0.2) (the velocity and the force-constant are so high, that i see something in little time). REF and ZUG are single atoms, and the two vectors (pull_vec1, pull_init1) are the vector from REF to ZUG. I tried it also with 'pull_start = yes' and 'pull_init1 = 0.0 0.0 0.0' and it worked. But i never tried the other 'pull_geometry'-options. ---------------------------------------------------- ; Pulling pull = umbrella pull_geometry = position pull_dim = Y Y Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = REF pull_group1 = ZUG pull_vec1 = -0.012 -0.174 1.794 pull_init1 = -0.012 -0.174 1.794 pull_rate1 = 0.01 pull_k1 = 5000 ------------------------------------------------------ Hope this helps Thomas ================================================================== Dear Thomas, I took you name from the gromacs mail list. It seems that you have been successful using the pulling in the new gromacs version. I used the 3.3 version for simulating afm pulling but I could not do it with the new code. All I want to do is constant velocity pulling group r_76 in the Z direction. I tried pulling r_1 to 001 and r_76 00-1 using the option for pull_ngroups =2, tried pull_geometry = position and nothing worked. It's a simple protein with 76 residues and solvated in water. I am attaching at the end of the message my last try of pulling options I really appreciate any suggestion you may have on this matter. Thanks!!!! Marisa Roman Physics Dept. Drexel University, Philadelphia ---------------------------------------------------------------- pull = umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = r_1 pull_group1 = r_76 pull_dim = N N Y pull_start = yes pull_k1 = 500 pull_kB1 = 500 pull_rate1 = 0.05 pull_vec1 = 0 0 1 pull_init1 = 0.0 pull_nstxout = 100 pull_nstfout = 100 =================================================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php