Re: [AMBER] md

From: Ilyas Yildirim <>
Date: Fri, 14 Jan 2011 09:16:25 -0600 (CST)

There are more than one ways to do it, but I think the most efficient way
is to run a test simulation first where you just neutralize the system.
Assuming you are going to do a constant pressure run, follow the
equilibration protocol. The volume will change pretty quickly to bring the
pressure to 1 atm. Plot the volume vs time to see if it converges to a
value. You can use that volume in your molarity calculation.

At this point, you should be able to know how many extra Na+/Cl- you
need for your system. You can use leap to add as many salt as you want but
I dont think this is the best way. What I would do is to use the last
snapshot of the equlibration MD. Check out how many water molecules there
are, and then randomly replace WAT with either Na+ or Cl-. Use iwrap=1 in
the equilibration, however, to make sure that everything is in the unit
cell. Now you have a system with a particular concentration. You should
start, again, the MD with minimization, and then do equilibration and
production runs.

Hope this helps.

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry - 2145 Sheridan Road =
   = Northwestern University - Evanston, IL 60208 =
   = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
   = =

On Fri, 14 Jan 2011, Ashutosh Shandilya wrote:

> 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

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Received on Fri Jan 14 2011 - 07:30:04 PST
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