Hi Tsjerk, Thanks for helpful advice. I decided to re-build my system from scratch, and I ran energy minimization again. This still ended badly, with a potential energy on the order of 10^8. Better than 10^18, but still not anywhere close to acceptable.
> My guess is that you've generated severe overlaps. On your starting > structure (the one you use as input to grompp) run trjconv -s in.gro > -f in.gro -o out.pdb -pbc inbox The out.pdb shows that some waters that were initially placed below the DPPC bilayer (crystal waters from the original structure) are now in a thin slab at the top of my box. I'm guessing this is a consequence of pbc, although these were not applied during my minimization steps. I centered my system in the box before beginning (edticonf -c), so I don't know how these residues escaped as a single unit. Also problematic is that there are water molecules inside the DPPC bilayer, and I'm wondering how they got there. Should I just delete these offending molecules and try to minimize again? Any thoughts? Thanks in advance; I've placed my minim.mdp file below this mail for your reference. Hopefully I'm not doing anything obviously wrong, I'm still very new to Gromacs. -Justin Justin A. Lemkul Department of Biochemistry Virginia Tech ----------------- minim.mdp ; LINES STARTING WITH ';' ARE COMMENTS title = 100-ps minimization of DPPC Bilayer with water box ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /usr/bin/cpp ; Preprocessor define = -DFLEX_SPC include = -I./ ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) dt = 0.002 ; Time step in ps emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform xtc_grps = system ; Which coordinate group(s) to write to disk energygrps = system ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 0.9 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 0.9 ; long range electrostatic cut-off rvdw = 0.9 ; long range Van der Waals cut-off pbc = no ; Periodic Boundary Conditions (yes/no) ; Parameters for temperature and pressure tau_t = 0.1 tc-grps = system ref_t = 323 tau_p = 5 ref_p = 1.0 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
