[gmx-users] Re: openmm

[Alan]

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<<