[gmx-users] (no subject)

[David]

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++