[gmx-users] Re: openmm
Alan
alanwilter at gmail.com
Wed Jul 29 14:45:24 CEST 2009
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 <alanwilter at 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 <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<<
>
--
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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