Hi, gmxusers My intention is to pull a group of silica to a membrane and output the force act upon the silica. I used the pull code as below:
pull = constraint pull_geometry = direction pull_start = yes ;pull_dim = N N Y pull_nstxout = 500 pull_nstfout = 500 pull_ngroups = 1 pull_group0 = DOPC pull_pbcatom0 = 4958 pull_group1 = MOL;silica pull_init1 = 0.0 pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 ;pull_k1 = 5000 I found using constraint always crash. some times a water cannot be settled. some times no error info output just crash. So I used an umbrella method to pull the silica, and a pull_K1 = 5000 is used. The mdrun went well. However, the traj is strange. At start the silica does not move, and suddenly it accelerate to more than 0.01 nm/ps can penetrate the membrane. Anyone could help me? Thanks. Di Cheng University of Science and Technology of China Hefei, Anhui Province 230026 P. R. China E-mail: [email protected] Tel.: +86-15321055911 -- 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
