[gmx-users] (no subject)
David
spoel at xray.bmc.uu.se
Wed May 25 18:46:26 CEST 2005
On Wed, 2005-05-25 at 16:57 +0100, M.Naser wrote:
> Hi David,
>
> Thank you very much for your reply.
>
> I am running the programme on AMP machines. I am not sure about the switch
> potential. Could you please explain a bit more about it?
Do you mean AMD?
Run 1 step of md with the -debug flag and look at the *tab files. For
Coulomb you don't want it but for Van der Waals it might be ok.
>
> With regards,
>
> Abu
>
>
> > On Wed, 2005-05-25 at 16:32 +0100, M.Naser wrote:
> >> Hi All,
> >>
> >> I have been running a system consisting 20368 atoms on a single node
> >> with
> >> the following parameters. The speed is about 3 days for a nano seconds.
> >> I
> >> have been wondering whether this is the expected speed in gromacs. I
> >> tried
> >> to run it on 4 nodes and unfortunately did not scale well. It appeared
> >> to
> >> be faster on a single node.Am I making any mistake along the line?
> >>
> > You can use constraints and take 2 fs timestep or dummies and
> > constraints and get 4 fs timestep.
> >
> > Also you don't say what machine you run on. It will be faster on SMP
> > machine with four CPUs. By the way are you sure you want a switch
> > potential?
> >
> >
> >> And also, is there any tool to count the hydrogen bond between protein
> >> and
> >> water molecule?
> > g_hbond
> >>
> >> Thanks in advance,
> >>
> >> Abu
> >>
> >> integrator = md
> >> dt = 0.001
> >> nsteps = 2000000
> >> tint = 0
> >> init_step = 0
> >> comm_mode = No
> >> nstcomm = 1
> >> nstlist = 10
> >> ns_type = grid
> >> pbc = full
> >> rlist = 0.9
> >> coulombtype = PME
> >> rcoulomb-switch = 0
> >> rcoulomb = 0.9
> >> vdwtype = switch;cut-off
> >> rvdw-switch = 0.8
> >> rvdw = 0.9; vdw/lj cutoff in nm
> >> fourierspacing = 0.12
> >> pme_order = 4
> >> ewald_rtol =1e-5
> >> ewald_geometry =3dc
> >> surface_epsilon =0
> >> optimize_fft =yes
> >> DispCorr = no
> >> table-extension = 1
> >> Tcoupl = Berendsen
> >> tc_grps = system
> >> tau_t = 0.1
> >> ref_t = 300
> >> Pcoupl = no
> >> pcoupltype = isotropic
> >> tau_p = 1.0
> >> compressibility = 4.5e-5
> >> ref_p = 1.0
> >> gen_vel = yes
> >> gen_temp = 300
> >> gen_seed = 284623
> >> constraints = none
> >> nstxout = 100
> >> nstvout = 100
> >> nstfout = 0
> >> nstlog = 100
> >> nstenergy = 100
> >> nstxtcout = 100
> >> xtc_precision = 1000
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> __________________________________________________________________
> >>
> >> DISCLAIMER:
> >>
> >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> >> __________________________________________________________________
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
>
>
> __________________________________________________________________
>
> DISCLAIMER:
>
> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> __________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list