Dear all, Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac and Windows so far, and it comes with examples, pretty neat.
Even though there's some apparently fixes compared to the usual release of openmm and gromacs-openmm, my molecule didn't work with it yet. Nevertheless, for those with nvidia cuda and Mac or Windows, it's worth trying. Cheers, Alan On Sat, Jul 18, 2009 at 18:31, Alan <[email protected]> wrote: > 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<< > -- 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<<
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