[gmx-users] Error of mdrun

Mark Abraham Mark.Abraham at anu.edu.au
Sat Apr 19 16:15:09 CEST 2008

s lal badshah wrote:
> Dear Mark,
> When I enter from root account the following is the result:
> linux:~ # which mdrun
> /sbin/mdrun
> linux:~ # which grompp
> /usr/bin/grompp
> linux:~ #
> But from user account the
>  which mdrun
> usr/bin/mdrun
> and also the
>  which grompp
> /usr/bin/grompp  
> occured.
> Actually I have very little experience with linux.I install VMD which 
> didn't open in user account but opened only in root account so I do MD 
> simulation in root accounts.If I do Md simulation from user account is 
> this problem arises or not? Is there any command so that mdrun also 
> operate in root account? A few mentioned in past mails archive of 
> gromacs didn't work as I used them.

Don't ever use the root account for daily usage. It's like driving your 
car while you haven't finished major maintenance.

If you follow the VMD installation instructions properly, it will work 
from user accounts, as with any other decent software. You should fix 
the cause of the VMD problem, or you'll only create more problems for 
yourself - such as the above. That said, you'll probably struggle to 
actually fix the existing consequences of your root usage... so 
re-installing the OS and starting again is a serious option.

These problems have nothing to do with GROMACS, so you should consider 
alternative sources of information on the web.


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