Hi I have a question regarding the implicit solvent implementation in GROMACS 4.5.1 (with GPU acceleration). I have been trying to simulate molecules with varying size (PYP with 125 AAs, BBA5 with ~20 AAs, and and Trigger Factor with 432 AAs), but can't seem to be able to maintain the secondary structure in any of them. Can any one suggest a particular set of parameters than need to be taken care of or used with certain fixed values for better results?
While I have used a varied range of values for almost all parameters, here is the list of parameters recently and unsuccessfully used: integrator = sd nsteps = 10000000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 10 comm_mode = Linear delta_t = 0.002 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = No nsttcouple = -1 epc = No epctype = Isotropic nstpcouple = -1 tau_p = 1 andersen_seed = 815131 rlist = 1.1 rlistlong = 2.5 rtpi = 0.05 coulombtype = Cut-off rcoulomb_switch = 0 rcoulomb = 2.5 vdwtype = Cut-off rvdw_switch = 0 rvdw = 2.5 epsilon_r = 1 epsilon_rf = 1 implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 1.1 gb_saltconc = 0.02 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Still sa_surface_tension = 2.092 shake_tol = 7.5e-06 bd_fric = 0.5 ld_seed = 2010 Thanks and Regards Kush -- Kushagra Singhal Promovendus, Computational Chemistry Universiteit van Amsterdam -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
