[gmx-users] Re: Secondary structure loss in implicit solvent simulations
Hi It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get these problems in explicit solvent simulations on CPU, only in implicit solvent simulations both on GPU as well as CPU. One of the problems that I can think of is unbalanced charges that I would have balanced out using NaCl ions, but not any more. Regards Kush -- Kushagra Singhal Promovendus, Computational Chemistry van 't Hoff Institute of Molecular Sciences Science Park 904, room C2.119 1098 XH Amsterdam, The Netherlands +31 205256965 Universiteit van Amsterdam k.sing...@uva.nl -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Secondary structure loss in implicit solvent simulations
Hi 1) I am using Amber03 forcefield. 2) In most cases Yes, but in others, implicit solvent simulations tend to crash almost immediately (after reporting segmentation fault). 3) It generally takes less than a couple of 100 ps for the loss of the secondary structure. A few times, I even received .gro files at the end with all values as "nan". Earlier I thought it might be a problem with equilibration, but I have tried to run energy-minimization more than once followed by position-restrained runs as well (to equilibrate H-atoms). But the end result hasn't changed. Thanks & Regards Kush --- Michael Shirts: A few questions: 1) What force field are you using? 2) do you get the same answers with and without GPU acceleration? 3) How long does it take for secondary structure to disappear? 100's of ps? 10's of ns? -- Kushagra Singhal Promovendus, Computational Chemistry van 't Hoff Institute of Molecular Sciences Science Park 904, room C2.119 1098 XH Amsterdam, The Netherlands +31 205256965 Universiteit van Amsterdam k.sing...@uva.nl -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Secondary structure loss in implicit solvent simulations
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 = 1000 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
