[gmx-users] Shake block errors with d.lzm

[David van der Spoel]

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
> 
> Thanks,
> Ganesh
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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