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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
