Re: [AMBER] question about calculated density in sander output file

From: David A Case <>
Date: Wed, 30 Nov 2016 14:39:05 -0500

On Wed, Nov 30, 2016, amaury paquet wrote:

> 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.

Have you checked that in the prmtop file itself the uranium masses are
correct? Does the sum of all the masses in the prmtop file add up to what
you think the total mass should be?


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Received on Wed Nov 30 2016 - 12:00:02 PST
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