Re: [AMBER] md

From: Jason Swails <>
Date: Fri, 14 Jan 2011 08:55:12 -0500

Look up the addions command in leap. It is well described in the AmberTools

To calculate salt concentration, you would calculate it the normal way. The
molarity is defined as moles of solute / liters of solution. Determine how
big you want your box to be, find the volume of that box (should be in cubic
angstroms), convert that to liters, then determine how many salt formula
units you want to add and convert that number to moles.

That should give you a good estimate. The volume will change slightly after
equilibrating at constant pressure, so you may have to recalculate the
volume after the box contracts to get the more accurate concentration.

Good luck,

On Fri, Jan 14, 2011 at 7:11 AM, Ashutosh Shandilya

> I wish to run Md simulation of a DNA on a 150 milimolar concentration. How
> to add salt in the solvent and how to calculate the concentration of
> solvent.
> Thanks and Regards
> *Ashutosh Shandilya*
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jan 14 2011 - 06:00:06 PST
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