[gmx-users] cluster

[Kushal Seth]

hi all !
I am trying to run the following command -
grompp -np 2  -v -f em.mdp -po emout-nowater -c
binaryCR-Ochol-box-largeZ.pdb -p mytop-nowater1.top -o em-nowater.tpr

but i am encountering this problem,


checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
 -I/usr/local/gromacs/share/gromacs/top  mytop-nowater1.top > gromppztCLJM'
' command is defined in the .mdp file
processing topology...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: grompp.c, line: 427

Fatal error:
number of coordinates in coordinate file (binaryCR-Ochol-box-largeZ.pdb,
10280)
            does not match topology (mytop-nowater1.top, 0)

Plz help me on this.
Thanks a lot in advance.


On 4/2/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Beniamino Sciacca wrote:
> > thanks.
> > but... another question: can i use a crossed network cable or a hub
> > instead the switch?
> > how can i say to gromacs to use both the pc?
> Cross cable should work if you can convince your OS that you have
> anetwork connection. search the website for running in parallel, e.g.
> mpirun is a good keyword.
>
>
> > thanks anymore, and sorry if the question isn't opportune enough
> >
> >
> >
> > David van der Spoel ha scritto:
> >
> >> Beniamino Sciacca wrote:
> >>
> >>> Hi!
> >>> I've a laptop with centrino duo, and a desktop with AMD 64 X2.
> >>> I've to work with my two pc in parallel. What have I to do?
> >>> can i use a net cable?
> >>
> >> not really a gromacs question but anyway.
> >> install the same OS on both (i.e. not 32 bit on the Intel and 64 bit
> >> on the AMD). Install LAM, and then Gromacs.
> >> Use network cables conected to a switch.
> >>
> >>
> >>> thanks
> >>> Beniamino
> >>>
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> >>
> >
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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
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