[AMBER] question about calculated density in sander output file

From: amaury paquet <amaury_paquet.hotmail.fr>
Date: Wed, 30 Nov 2016 14:22:01 +0000

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.

PhD student

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Received on Wed Nov 30 2016 - 06:30:02 PST
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