David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 20 20:11:43 CEST 2010
On 2010-09-20 19.58, nishap.patel at utoronto.ca wrote:
> I am simulating 2M urea in water with single methane (77 urea + 1926
> water). I used genbox -ci -nmol to add the number of urea molecules and
> then used genbox to add water molecules (as suggested in the manual).
> When I tried to do energy minimization this is what I got :
> Steepest Descents converged to Fmax < 1000 in 234 steps
> Potential Energy = -1.0054066e+05
> So I tried g_energy to plot the potential. But I got average Potential
> as a positive number 2.84087e+06. I am not sure why the potential is
> positive, it probably is because of repulsion but is that correct?
Did you look at the graph? Please do, then you will understand.
> I would appreciate some help.
> -Nisha P
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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