I've been searching for an answer to this question for years, and I'm shocked I haven't found any discussion on any forums. Here is an example to provide more details:
I am preparing a 450 residue protein for simulation. I use tleap to solvate a rectangular box with a 12 Å buffer. > solvatebox mol TIP3PBOX 12
After adding the explicit waters, tleap reports that the volume is 707367.032 Å^3 and the density is 0.833 g/mL, rather than an expected 0.998 g/mL.
It seems that the density is always around 0.85 g/mL.
Therefore I have two questions:
1.) Why does tleap do this?
and
2.) How do you work around this? Right now, my personal workflow is to calculate a corrected volume (i.e., what would the volume need to be to have a 0.998 g/mL density) and use that value to calculate how many ions to add in order to reach my desired ionic concentration for simulation. Then during my equilibrium process of the simulation I allow the box volume to adjust. In the end, during production runs the density is accurate, therefore this problem does not impact my analyses, however it still annoys me.
Thanks for you input!
Thanks for the question and I apologize for the answer as I am a specialist in the agricultural field
Finally found some response to this:
http://ambermd.org/Questions/leap.html
Long story short, if you use tleap to solvate you need to run an equilibration in NPT so allow for the volume to adjust.
What I want to point out then is that when decided how many ions you need to add to achieve a desired ionic concentration you should NOT base your calculation on the initial box volume, the volume listed in tleap. You should base it off the number of water molecules.
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