Well, not coiled coil, but I have observed serious distortions in a all-helix protein with G53A6 and reaction field. Using PME solved the problem.
Marcos On Mon, 2009-07-20 at 13:50 +0200, Lory Montout wrote: > Dear all > > I recently performed MD simulations using 53A6 force field with > Gromacs4.0 The system includes a protein+water and ions for > neutralizing, The protocol is quite classical: NPT ensemble, 300K and > reaction field for electrostatics, 2fs for integration, bond lengths are > constrained. > The protein is a coiled-coil fiber like protein, including different > repeat units. At the > starting point, the protein roughly adopts a cylinder shape. After > few ns ( less than 5), some helices are broken, even unfold. Finally, > the protein is kinked,with a kink angle ~ 90°. I tested different > constructions but observed similar results. > The same system was simulated with NAMD, charmm force field, the > structure remains stable all along the simulation (10ns for now ). > Did anyone obtain similar results for a coiled coil system with 53A6 > force field? > > here is my .mdp file : > > nstvout = 10000 > nstfout = 0 > nstxtcout = 2500 > xtc_precision = 1000 > nstlog = 500 > nstenergy = 500 > nstlist = 5 > rlist = 0.8 > coulombtype = generalized-reaction-field > rcoulomb = 1.4 > rvdw = 1.4 > epsilon_rf = 62.0 > ; Temperature coupling is on in two groups > Tcoupl = Berendsen > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Energy monitoring > energygrps = Protein SOL NA+ > ; Pressure coupling is not on > Pcoupl = Berendsen > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > > Thanks a lot for your answers._______________________________________________ > 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 _______________________________________________ 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