[gmx-users] Re: openmm
Alan
alanwilter at gmail.com
Wed Jul 29 18:44:18 CEST 2009
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 <alanwilter at gmail.com> 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 <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<<
>
--
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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