[gmx-users] Re: openmm
Alan
alanwilter at gmail.com
Tue Jul 28 16:04:32 CEST 2009
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 <alanwilter at 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<alanwilter at 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<alanwilter at 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-request at 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<<
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