Hi everyone I am currently trying to perform a peptide-ligand (~4000 and 110 Da respectively) simulated annealing study using gromacs (5.1.2) with Amber force fields. Under the initial energy minimization step (minim.mdp and nvt.mdp) I am finding that the step fails. It then kicks out pdb files, which when opened depicts a ligand that has 'exploded' with the peptide fragmented into a number of pieces.
Under the same conditions, I can get the peptide to run with a ligand about twice the size of the above, which follows through to completion of all annealing steps to gain output pdb files. Accounting for a peptide only system, the peptide will also follow through to completion. Is anyone able to suggest how to optimize the minim/nvt files, or make sense of the log file. I have linked to the minim, nvt and output log files below. minim https://www.dropbox.com/s/80wwe8n2ncpg77t/minim.mdp?dl=0 nvt https://www.dropbox.com/s/qruyanl8vg1a3no/nvt.mdp?dl=0 Log details (md_temp.e20786725) https://www.dropbox.com/s/0fnjm05ub85yiun/md_temp_e20786725.txt?dl=0 Any help would be greatly appreciated. Richard -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
