[gmx-users] (no subject)

[M.Naser]

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?

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
>>
>>
>>
>>
>>
>>
>>
>>
>> __________________________________________________________________
>>
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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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