[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

[Justin Lemkul]

On 3/2/13 1:42 AM, swati rana wrote:
> Hi Justin,
>
> Thanks a lot, that suggestion of yours helped. I am on the equilibration
> step and its running but nothing is happening on the terminal its just
> stagnant. Is it fine because its more than 17 hrs now. Is there some
> problem.
> After running the second command nothing is happening on the terminal.
>
> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>
> mdrun -deffnm nvt
>
> I am sorry as it is not a reasonable question to ask but i am just asking
> out of curiosity and lack of time.
>

If you're trying to run an MD simulation in serial, you'll get terrible 
performance unless the system is very small (a few hundred atoms).  Most MD is 
conducted in parallel on high-performance computing clusters, or at the very 
least on a multi-core workstation, again using parallelization.

You won't get constant output in either case, since I/O is buffered and write 
intervals depend on what you specify in the .mdp file.  In any case, if you're 
getting poor performance, you're probably simply asking your computer to do 
something it's incapable of handling efficiently.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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