[gmx-users] grompp

[Mark Abraham]

主月 ：） wrote:
> Hi:
> I've installed GROMACS for single and parrel in my clusters. And these two version are stalled in /home/gromacs_s/ and /home/gromacs_p/ respectively and both of them are not linked.
> 
> When i used the single version, every thing is ok.But when i used parrel version trouble is coming.
> If i qsub with more than 1 node ,the outfile tell me the follows!(if i qsub with 1 node it is ok)
> 
> 
> 
> 
> Reading file topol.tpr, VERSION 3.3 (single precision)
> -------------------------------------------------------
> Program mdrun, VERSION 3.3
> Source code file: init.c, line: 69
> 
> Fatal error:
> run input file topol.tpr was made for 1 nodes,
>              while mdrun expected it to be for 5 nodes.

mdrun expected it to be for 5 nodes (presumably) because you gave it the
"-np 5" command line argument. However you need to anticipate this when
you use grompp in order to construct a .tpr file that is for 5 nodes by
giving the same command line argument. See the manpage for mdrun.

Mark