[gmx-users] Shake block errors with d.lzm
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jan 24 16:44:44 CET 2008
Ganesh CN wrote:
>> you can not use so many processors for such a small system in 3.3. In
>> 4.0 you will be able to do it.
> Thanks for your response David. Is it possible to scale up the
> problem size so that I can run it on 16 or more processes ? If so,
> could you let me know what parameter I have to change to scale up ?
> (I am not too conversant with the molecular dynamics principles - so
> please forgive my ignorance). Or is there is some other input file
> which will work for 16 processes ? I am using cutoff.mdp as pasted
> below :
use more water :)
> title = dppc
> cpp = /lib/cpp
> integrator = md
> nsteps = 5000
> nstlist = 5
> nstxout = 0
> nstvout = 0
> nstxtcout = 0
> nstlog = 0
> dt = 0.004
> constraints = all-bonds
> nstenergy = 0
> ns_type = grid
> coulombtype = cut-off
> rlist = 0.9
> rvdw = 1.4
> rcoulomb = 1.4
> tcoupl = berendsen
> tc_grps = protein cl- sol
> tau_t = 0.1 0.1 0.1
> ref_t = 300 300 300
> Pcoupl = no
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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