Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp?
ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented My full md.mdp file is: integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist = 1.0 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 comm_mode = ANGULAR Many thanks in advance, Alan On Sat, Jul 18, 2009 at 11:35, Alan<[email protected]> wrote: > Dear Mark, > > Thanks. I reread those file carefully and noticed the "only implicit > solvent". Sorry for that. I am building my test case here to see by > myself how fast it can be. > > Alan > > > On Sat, Jul 18, 2009 at 11:00, <[email protected]> wrote: > >> Alan wrote: >>> Hi list, does anyone have an example (input pdb, gmx commands and >>> md.mdp for example) to test gromacs with and without openmm? >>> >>> The case I use here (with explicit water) didn't show me any speed up >>> (comparing with mpirun -c 2 mdrun_mpi...). >>> >>> I am using Mac Leopard 10.5.7 with Cuda drivers and gromacs 4.0.5 >> >> This would be expected if you read the OpenMM README.... or see >> http://oldwiki.gromacs.org/index.php/OpenMM_GROMACS >> >> Mark > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>>http://www.bio.cam.ac.uk/~awd28<< > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< _______________________________________________ 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
