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

[swati rana]

Dear Justin,

Thanks a lot, your suggestions helped me a lot.

With Regards,
Swati


On Sun, Mar 3, 2013 at 1:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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