From owner-chemistry@ccl.net Wed Apr 29 07:12:01 2015 From: "James Buchwald buchwj() rpi.edu" 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 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 29 Apr 2015 01:57:39 -0400 MIME-Version: 1.0 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> > From owner-chemistry@ccl.net Wed Apr 29 12:48:01 2015 From: "Safiya Ess Amer amersaf85[a]yahoo.com" To: CCL Subject: CCL:G: Wave Function and format in G03W Message-Id: <-51328-150429122532-22674-UgyBqxyIXXY+CHIIwqk8Cw^^^server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Wed, 29 Apr 2015 12:25:31 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85_._yahoo.com] Hello everyone, I have two questions first regarding how to control format of output of Gaussian03, Especially decimal places (i.e. number of digits after a point) in Summary of Optimized Potential Surface Scan. second about wave function using G03W, I am using keyword pop=full or pop=regular with creating check point file,finally viewing wave function using GaussView. my question is there any other keywords can be used for get best results about wave function. Any suggestions? Thanks in advance Safiya Amer Graduate Student amersaf85(a)yahoo.com h2feoh3(a)gmail.com From owner-chemistry@ccl.net Wed Apr 29 16:05:01 2015 From: "rjensen]=[ualberta.ca" To: CCL Subject: CCL: Determining appropriate simulation volume from solubility data Message-Id: <-51329-150429155637-2465-8xAWJwsEBvsuSWVyvbANRQ+/-server.ccl.net> X-Original-From: rjensen#%#ualberta.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 29 Apr 2015 13:56:26 -0600 MIME-Version: 1.0 Sent to CCL by: rjensen^_^ualberta.ca Two papers that may be of interest: A computational study that you are likely aware of. J. Chem. Phys. 2003, 119, 8038. Experimental determination of hydration spheres from salt solubility. J. Phys. Chem. B 2001, 105, 7805. Dr. Roy Jensen (==========)-----------------------------------------¤ Lecturer, Chemistry W5-19, University of Alberta 780.248.1808 On Wed, 29 Apr 2015 01:57:39 -0400, you wrote: > >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