[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
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> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
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> >
> 
> 
> 
> __________________________________________________________________
> 
> DISCLAIMER:
> 
> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> __________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
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-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++




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