Tutorial 2: entropy of mixing of methanol+water - Revision history

Miguel Caro: /* Input files */

2017-12-28T12:20:56Z

‎Input files

2017-04-29T11:00:24Z

2017-04-25T13:44:06Z

‎Generating the trajectories

2017-04-25T13:42:31Z

‎Trajectories for analysis with DoSPY

2017-04-25T13:41:46Z

‎Generating the trajectories

2017-04-25T11:00:01Z

‎Homework

2017-04-25T10:59:31Z

‎Homework

2017-04-25T10:58:10Z

‎Computing the excess entropy of mixing

2017-04-25T10:55:43Z

‎Computing the excess entropy of mixing

2017-04-25T10:46:27Z

‎Extracting the entropies

@@ Line 220: / Line 220: @@
   for i in range(0,nmet):
       print 6,1
-      print nwat*3+i*6+1, nwat*3+i*6+2, nwat*3+i*6+3
+      print nwat*3+i*6+1, nwat*3+i*6+2, nwat*3+i*6+3, nwat*3+i*6+4, nwat*3+i*6+5, nwat*3+i*6+6
 and run

← Older revision		Revision as of 11:00, 29 April 2017
Line 1:		Line 1:
−	~~'''This tutorial is currently under construction'''~~
−
	When two pure liquids are put in contact the new configurations that the molecules can adopt and the new molecular interactions will lead to a change in entropy. Typically, this change is positive because of disorder, although in principle specific molecular interactions can lead to a decrease in entropy in some cases. For ideal gases, the entropy of mixing has an analytical expression, and it depends only on the relative number of molecules of each component in the mixture. The total entropy of a mixture of ideal gases is:		When two pure liquids are put in contact the new configurations that the molecules can adopt and the new molecular interactions will lead to a change in entropy. Typically, this change is positive because of disorder, although in principle specific molecular interactions can lead to a decrease in entropy in some cases. For ideal gases, the entropy of mixing has an analytical expression, and it depends only on the relative number of molecules of each component in the mixture. The total entropy of a mixture of ideal gases is:

@@ Line 15: / Line 15: @@
 For this tutorial we will use Gromacs to generate the mixture of liquids and the pure liquids. We will use the OPLS force field and the SPCE water model. For methanol we will use the topology available from [http://virtualchemistry.org virtualchemistry.org]. We will constrain all bonds with H atoms.
-You can skip this section and download the trajectories that we will be analyzing from [https://doi.org/10.5281/zenodo.567867 Zenodo]. Then continue with the 2PT analysis section.
+'''You can skip this section and download''' the trajectories that we will be analyzing from [https://doi.org/10.5281/zenodo.567867 Zenodo]. Then continue with the 2PT analysis section.
 === Generating the starting configurations ===

@@ Line 169: / Line 169: @@
   gmx mdrun -v -deffnm md
-=== Trajectories for analysis with DoSPY ===
+=== Trajectories for analysis with DoSPT ===
 Now you can save this system equilibrated in the NVT ensemble:

@@ Line 15: / Line 15: @@
 For this tutorial we will use Gromacs to generate the mixture of liquids and the pure liquids. We will use the OPLS force field and the SPCE water model. For methanol we will use the topology available from [http://virtualchemistry.org virtualchemistry.org]. We will constrain all bonds with H atoms.
-You can skip this section and download the trajectories that we will be analyzing. Then continue with the 2PT analysis section.
+You can skip this section and download the trajectories that we will be analyzing from [https://doi.org/10.5281/zenodo.567867 Zenodo]. Then continue with the 2PT analysis section.
 === Generating the starting configurations ===
@@ Line 193: / Line 193: @@
 This [[Tutorial2_script|bash script]] should allow you to run all the dynamics above with minimal human intervention once your initial structures "pure_water.gro", "pure_methanol.gro", "mixture_1.gro", etc. have been generated.
 == DoSPT analysis ==

@@ Line 396: / Line 396: @@
 We didn't check the statistical variation of the pure liquid, which can in fact be large for methanol. Check the effect of that quantity on the final result.
+You can also check the effect of using different combinatorial entropy of mixing ([[entropy_mixture]] tag) and diffusivity models ([[hs_formalism]] tag) on the results.
 == References ==
 {{Reference list}}

@@ Line 388: / Line 388: @@
 <math>
-\bar{S}^\text{E}_\text{mix} = \bar{S}_\text{mixture} - \frac{400}{600} \bar{S}_\text{wat} - \frac{200}{600} \bar{S}_\text{met} + k_\text{B} \frac{400}{600} \ln{\left( \frac{400}{600} \right)} + R \frac{200}{600} \ln{\left( \frac{200}{600} \right)},
+\bar{S}^\text{E}_\text{mix} = \bar{S}_\text{mixture} - \frac{400}{600} \bar{S}_\text{wat} - \frac{200}{600} \bar{S}_\text{met} + R \frac{400}{600} \ln{\left( \frac{400}{600} \right)} + R \frac{200}{600} \ln{\left( \frac{200}{600} \right)},
 </math>
-where <math>R = 8.314</math> J/mol/K is the gas constant (<math>R = N_\text{A} k_\text{B}</math>).
+where <math>R = 8.314</math> J/mol/K is the gas constant (<math>R = N_\text{A} k_\text{B}</math>). The final result is <math>\bar{S}^\text{E}_\text{mix} = -3.2</math> J/mol/K. The experimental value is approximately <math>-3.8</math> J/mol/K.<ref name="lama_1965"/>
 == References ==
 {{Reference list}}

@@ Line 382: / Line 382: @@
   Raw: 82.5 +- 0.5 J/mol/K
   Ren: 82.2 +- 0.2 J/mol/K
 == References ==
 {{Reference list}}