[gmx-users] IRIX PROBLEMS

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 9 16:03:01 CET 2003

On Tue, 2003-12-09 at 14:23, Raj Badhan wrote:
> In reply to David response, thank you for replying and giving me 
> some clue to the problems!
> If I am unable to run EM in parallel, how would I run this?
> What I mean to ask, is that if I ran this on a single processor, and 
> then with the output used that to solvate/full MD sim. the software 
> would complain that the input files were made for a single node 
> when I request the simulation to run on multiple processors. How 
> would I overcome this?

as long as you use the output confout.gro file from EM there is no

> Is there any way to transfer everything I do upto the point of the 
> final simulation from a single processor machine to the 
> supercomputer and run the program with say 8 or 16 processors?
> Also, they have installed the double precision version, which I 
> believe is only required under certain circumstances, could this 
> cause any problems?
> Many thanks to you all for your assistance.
> Raj Badhan
> Postgraduate researcher
> School of Pharmacy and Pharmacetical Science
> The University of Manchester
> Manchester, UK.
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David van der Spoel, PhD, Assist. 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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