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 <alanwil...@gmail.com> 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 <alanwil...@gmail.com> 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<alanwil...@gmail.com> 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<alanwil...@gmail.com> 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, <gmx-users-requ...@gromacs.org> 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<<
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