From owner-chemistry@ccl.net Wed Apr 29 07:12:01 2015
From: "James Buchwald buchwj() rpi.edu" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: Determining appropriate simulation volume from solubility data
Message-Id: <-51327-150429015703-28456-fA+22vO2sbYOEdAewBZhOw##server.ccl.net>
X-Original-From: James Buchwald <buchwj()rpi.edu>
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Date: Wed, 29 Apr 2015 01:57:39 -0400
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Sent to CCL by: James Buchwald [buchwj- -rpi.edu]
Conor,

Perhaps you could try converting from mg/mL to mole percent.  This will 
give you an idea of what is contained in the simplest "unit cell" of 
your solution - 1 molecule of analyte per x molecules of water.  Then 
you could construct an arbitrary cell meeting that mole specification, 
and then "relax" the cell in a simulation with periodic boundary 
conditions (and the appropriate thermodynamic ensemble and corresponding 
parameters) to obtain a representative unit cell.  If you use a 
well-tuned solvation code (I know GROMACS has a command line one, and 
UCSF Chimera has a graphical tool for doing this), you can generate an 
initial solvation box with the appropriate number of waters that will be 
"relatively" close to the target relaxed cell.  The advantage of this 
approach is that you preserve (in a certain sense) the "concentration" 
of the solution.

Best,
James

-- 
James R. Buchwald
Doctoral Candidate, Dept. of Chemistry and Chemical Biology
Rensselaer Polytechnic Institute
Graduate Researcher, Dinolfo Laboratory
Teaching Assistant, Experimental Chemistry IV


On 4/28/2015 1:35 PM, Conor D parks coparks2012(0)gmail.com wrote:
> Sent to CCL by: "Conor  D parks" [coparks2012[]gmail.com]
> Hello everyone,
>
> I have a question regarding how to determine the appropriate simulation cubic box length given a
> solubiliy data point. For instance in the crystal simulation literature, I frequently see something
> like "we simulated a solvated glycine crystal in a solution of 300 mg glycine/ml water." My
> question is what exactly is meant by ml water here for molecular dynamics? Am I to interpret the
> ml water as the simulation total volume? Without knowledge of what the total solution density is,
> with mixing effects included, how am I to determine what the appropriate box volume from is this
> information? As a first guess, I am thinking of taking a glycine crystal with 1024 molecules,
> interpreting the ml water as total simulation volume, and just solvating the box with water
> molecules. Any suggestions?
>
> Conor>
>