[gmx-users] Urea-water

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon Sep 20 20:27:16 CEST 2010

I did look at the plot, and it shows that the curve is smoothing right  
under zero at -1.00e+05 but then why does the average potential show a  
positive number? Shouldn't that number be negative as well?

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On 2010-09-20 19.58, nishap.patel at utoronto.ca wrote:
>> Hello,
>> 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.
>> Thanks.
>> -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.
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