Thanks Justin. I could swear I tried what you said... anyway it worked now (2.5 x faster), but not with implicit solvent for mdrun-openmm... Trying with plain mdrun with the setup for implicit solvent and it seemed to work (although I don't know how to interpret this from GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: "even though this is not available in the standard Gromacs 4")
I still would like an example/tutorial that really worked for someone with gmx openmm. In the end, with mdrun-openmm and implicit solvent in the mdp file, I got a file md.gro full of "nan nan". For those interested, here are the commands I did. If you have GMX with ffamber, CUDA and GMX-openmm you may reproduce it. ############################### cat << EOF >| em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol = 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = Reaction-Field ns_type = simple rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step epsilon_rf = 0 pbc = no EOF cat << EOF >| md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist = 1.2 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 comm_mode = ANGULAR ; uncomment below to test with implicit solvent ;implicit_solvent = GBSA ;gb_algorithm = OBC ;gb_epsilon_solvent = 78.3 EOF wget -c "http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG"; -O 1BVG.pdb grep 'ATOM ' 1BVG.pdb>| Protein.pdb grep 'HETATM' 1BVG.pdb>| Ligand.pdb sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \ | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \ | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \ | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g >| ProteinAmber.pdb # Process with pdb2gmx and define water pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -ignh grompp -f em.mdp -c Protein2.pdb -p Protein.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr # OK mdrun-openmm -v -deffnm md # 3 times fater # works fine without set for implicit solvent in md.mdp # with implicit solvent, md.gro full of nan nan nan everywhere. ############################### On Sat, Jul 18, 2009 at 17:31, Alan<[email protected]> wrote: > 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<< > -- 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
