Hi Yao Yao,
> Just kind of confused about the final system pressure in 1st DNA
> tutorial.
>
> I used the process_mdout.perl to process the polyAT_wat_md2.out,
> although the xmgrace plot for the pressure looks the same, but I found
> summary_avg.PRES shows -81.6 and summary_rms.PRES shows 301.7.
>
> I realized it is just a short 120 ps test run, but is it safe for me to
> conclude that the system is stable with
> 1 bar pressure?
>From the numbers you give no you cannot conclude this. The system is stable
at 1 bar pressure when the average is 1 bar. What you see here is a negative
average pressure. While this does not make physical sense what it means in
terms of the calculation is that the box size should shrink. If you plot the
density you will likely see that the density has not converged. It is still
climbing. This is because the simulation is too short. You probably need to
run a few nanoseconds to converge the density you then find that the average
pressure, taken over the last few nanoseconds of the trajectory should have
an average much closer to 1.
I hope this helps.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Oct 28 2011 - 12:30:02 PDT
