Hi
I have questions about running simulations with sander. Does somebody could tell me how the density of the simulation box is calculated in the output file of the simulation ?
My problem is I have a box with an average density of 0.90 according with the output file. The experimental density of the simulated solution is about 0.94 but if I divide the total mass of molecules in my box with the volume given in the output file I find 0.95 as density. This result is closer to the experimental density. What's weird is that more I have cations in my box more there is a difference between the density given in the output file and the density I calcul myself. The cation that I simulate is UO2+
Uranium is not in the PARM99 file that we use so we have created a .PARM file for uranium. But we checked this file, masses are correct.
If someone has an idea of where could be the problem it would be very helpful.
Amaury PAQUET
PhD student
amaury_paquet.hotmail.fr<mailto:amaury_paquet.hotmail.fr>
amaury.paquet.cea.fr<mailto:amaury.paquet.cea.fr>
France/CEA
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Received on Wed Nov 30 2016 - 06:30:02 PST
