Dear Mark, I've contacted the authors already. I decided to publish here as well just to close this topic.
Alan On Wed, Jul 29, 2009 at 13:45, Alan <[email protected]> wrote: > As I found out by test&error myself, mdrun-openmm will not work with > systems with more than one chain. > > Cheers, > Alan > > On Tue, Jul 28, 2009 at 15:04, Alan <[email protected]> wrote: > >> 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<< >> > > > > -- > 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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