Dear GROMACS users, I'm trying to do this tutorial with 1ijy structure from rcsb.org All .gro files on different step raise questions. 1) conf.gro - by VMD I see some strange groups which are not linked with the protein. 2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this? 3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems...
The .gro files are in the attachment. On minimization step I also get: Steepest Descents converged to machine precision in 73 steps, but did not reach the requested Fmax On equilibration step I also get an error(with such .gro file it very proabable): Warning: 1-4 interaction between 2 and 19 at distance 2.795 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 0.000 ps: Water molecule starting at atom 33175 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1# Wrote pdb files with previous and current coordinates step 0Segmentation fault Best regards, Andrew _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
