Dear Justin, dear Luca, here's the answer to your questions: - I'm currently using the "classical" forcefield gromos96 43a1 (choice "0" in pdb2gmx). After producing the topology, the only warning I see from pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and 63 atoms with occupancy unequal to one (out of 1583 atoms). Check your pdb file. However, atoms with occupancy <1 are present also in "regular" PDB files (if I remember well, also in PDB files I used previously). Is this a problem? - Box: I'm currently using a cubic box and I'm setting 1 nm of distance between solute and box with option -d (and also center the box). Looking at the system I can't see any contact between the protein and the box walls. I started by setting 0.8 nm and the problem was the same. - .mdp file: here it is: cpp = define = -DFLEXIBLE constraints = none integrator = steep nsteps = 50000 emtol = 1000 emstep = 0.1 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no gen_vel = no It's very similar to the one Justin suggested in its tutorial. - PR-MD: I'not interested in skipping the minimization and continue with MD. I tried to launch a PR-MD step to see if the error produced in this step was more informative, and try to understand what was the problem on my structure. I failed, however...
I would also add that this is not the first time that I'm using an homology model produced by MODELLER to perform MD. All the checks I made on my model tell me that it is a good model, so I really don't understand what's wrong with it. Finally, I started from the structure deprived of the first residue in order to see if that residue was the "bad" one, but the problem still persists and the potential energy has the same negative value with the same order of magnitude. Anna -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
