Hi there, I am trying to simulate a protein using a GBSA (implicit solvent) approach, and first I've been googling a bit in order to set the parameters of the simulation (mdp file) as better as possible.
I am using the following mdp options for the minimization step (the parameters of the Implicit Solvent section are also set in the subsequent NVT and NPT steps): -------------------------------------------------------------------------------- title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = cutoff_scheme = group ; Parameters describing what to do, when to stop and what to save integrator = steep emtol = 1.0 emstep = 0.01 dt = 0.001 nsteps = 40000 nstenergy = 500 energygrps = System ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = simple coulombtype = cut-off rcoulomb = 0 vdwtype = cut-off rvdw = 0 constraints = none pbc = no ld-seed = 10000 nstlist = 0 rlist = 0 comm-mode = angular comm-grps = Protein optimize_fft = yes ; Implicit solvent implicit_solvent = GBSA gb_algorithm = OBC gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 nstgbradii = 1 rgbradii = 0 gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm = ace-approximation ---------------------------------------------------------------------- The point is that after this minimization step I am obtaining a protein where the alpha helixes seem to be something relaxed or extended in an unusual way at least compared to when explicit solvent is used. This fact, i.e. such a local structural weakening, lead then to a fast protein unfolding during the subsequent NVT and NPT steps something that I am sure is not normal that soon. So, my question is whether there is someone over there has performed simulations combining CHARMM27 force field and a GBSA approach and has happened the same? Is there any incompatibility between them using GROMACS? I could find some papers in which this combination is used but using NAMD. Any help or advise would be appreciated so much. Thank you!! Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and Physics of Complex Systems (BIFI) Mariano Esquillor, Edificio I + D - 50018 Zaragoza (Spain) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.