[gmx-users] Urea-water

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon Sep 20 19:58:58 CEST 2010


    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?

I would appreciate some help.


-Nisha P

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