Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG.
I have tried the cg protein alone genbox -cp my.pdb -box 15 -o my.gro grompp -f em.mdp -c my.gro -p my.top -o topol.tpr mdrun -v -s topol.tpr steepest descents converged to machine precision but not to the requested Fmax < 2000 Pot Ener 7.1e+08 Max force 6.1e+10 on atom 983 Norm of force 2.5e+11 confout.gro shows that one of the subunits has been displaced from the multimer (apparently both intact) There is a long bond between the displaced subunit and the rest of the multimer, very closely to the atom 983 of max force, located in the pore region. I have scarce experience with gromacs yet, hope that this suggests remedies. I used a crude version of em.mdp. thanks francesco ---------- Forwarded message ---------- From: Francesco Pietra <francesco.pie...@accademialucchese.it> Date: Mon, Nov 30, 2009 at 5:36 PM Subject: Last step before CG em.mdp To: Discussion list for GROMACS users <gmx-users@gromacs.org> Hi: This is to ask how to proceed to minimize a CG ensemble made of a transmembrane multimer with pore region immersed in a hydrated DPPC bilayer and extracellular region immersed in water. Total height 18 nm, width 10 nm in the extracellular region and 6 nm in the pore region. No clashes/contacts at 1 Angstrom vdw overlap. That is, cavities had been created - in two steps - with 2.5 Angstrom margin into both the bilayer surrounding the pore and the water surrounding the extracellular region. Everything worked fine up to creating the topol.tpr, perhaps using a too small -box 15 15 15. Minimization by steepest descents (em.mdp below) cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no gave Pot ener 6.6e+15 Max force inf on atom 370 Badly, confout.gro shows the ensemble destroyed, the pieces lying along a straight line with the water box (that originally surrounded the extracellular region) at the center. The commands: genbox -cp my.pdb -box 15 15 15 -o my.gro and then the system topology with grompp -f em.mdp -c my.gro -p my.top -o topol.tpr and then mdrun -v -s topol.tpr ============== I found no way to build the system using gromacs scripts alone, i.e., combining preformed gromacs canonical boxes. The way I described above works fine in Amber with all-atom ensemble. ========== I would appreciate very much an opinion about the feasibility of such an approach with gromacs, or, hopefully, if a further solvation step is needed before minimizing. I did not try with a larger box, or if the protein+DPPC alone should be solvated with gromacs commands (I avoided this way because I want to leave the DPPC not solvated from the sides)... Thanks for answering francesco pietra -- 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