Recent changes to MoreThanOneSolute

MoreThanOneSolute modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 18 Oct 2024 01:56:06 -0000

--- v2
+++ v3
@@ -11,7 +11,6 @@
 The soln/MDinfo file then reads

 ~~~~
-::::text
 (number of frames) 2
 100 900
 9 3
@@ -31,7 +30,6 @@
 The refs/MDinfo file is then

 ~~~~
-::::text
 (number of frames) 2
 99 900
 9 3
@@ -39,7 +37,6 @@
 when the solute is EtOH, and it is

 ~~~~
-::::text
 (number of frames) 2
 100 899
 9 3

MoreThanOneSolute modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 18 Oct 2024 01:55:44 -0000

--- v1
+++ v2
@@ -1,11 +1,8 @@
 Finite concentration of solute: when more than one molecules are present for the solute species
 ----
-
-The followings are effective as of ver 0.3.alpha4.
-
 Suppose that the soln system consists of 100 EtOH molecules and 900 water molecules.
 When EtOH is the solute, one of the 100 EtOH molecules is actually treated as the 'solute' and the other 99 are treated as part of the mixed solvent; the mixed solvent consists of 99 EtOH molecules and 900 water molecules.
-For a single snapshot of the soln system given above, ermod performs 100 samplings of solute-solvent configuration.
+For a single snapshot of the soln system given above, erdst performs 100 samplings of solute-solvent configuration.
 In the 1st sampling, the 1st EtOH molecule is treated as the solute, and the solute-solvent interactions of the solute EtOH are calculated against the 99 'solvent' molecules of the 2nd to 100th EtOH molecules as well as against the 900 water molecules.
 In the 2nd sampling, the 2nd EtOH molecule is treated as the solute, and the solute-solvent interactions of the solute EtOH are calculated against the 99 'solvent' molecules of the 1st and the 3rd to 100th EtOH molecules as well as against the 900 water molecules.
 And the 3rd to 100th EtOH molecules are treated similarly.
@@ -25,7 +22,7 @@
 When the number of solute molecules is larger than 1, though, MolPrm1 is the same as SltInfo and is not necessary.
 MolPrm2 is necessary since it has the force-field parameters of water.

-Similarly, when the water molecules is the solute, ermod performs 900 samplings of solute-solvent configuration for a single snapshot of the soln system given above.
+Similarly, when the water molecules is the solute, erdst performs 900 samplings of solute-solvent configuration for a single snapshot of the soln system given above.
 The necessary force-field inputs are then SltInfo and MolPrm1.
 MolPrm1 corresponds to EtOH. MolPrm2 is for water and is the same as SltInfo when water is the solute.

@@ -49,3 +46,4 @@
 ~~~~
 when the solute is water.

+The above is effective as of ver 0.3.alpha4.

WikiPage MoreThanOneSolute modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Wed, 09 Jan 2013 07:24:24 -0000

Finite concentration of solute: when more than one molecules are present for the solute species

The followings are effective as of ver 0.3.alpha4.

Suppose that the soln system consists of 100 EtOH molecules and 900 water molecules.
When EtOH is the solute, one of the 100 EtOH molecules is actually treated as the 'solute' and the other 99 are treated as part of the mixed solvent; the mixed solvent consists of 99 EtOH molecules and 900 water molecules.
For a single snapshot of the soln system given above, ermod performs 100 samplings of solute-solvent configuration.
In the 1st sampling, the 1st EtOH molecule is treated as the solute, and the solute-solvent interactions of the solute EtOH are calculated against the 99 'solvent' molecules of the 2nd to 100th EtOH molecules as well as against the 900 water molecules.
In the 2nd sampling, the 2nd EtOH molecule is treated as the solute, and the solute-solvent interactions of the solute EtOH are calculated against the 99 'solvent' molecules of the 1st and the 3rd to 100th EtOH molecules as well as against the 900 water molecules.
And the 3rd to 100th EtOH molecules are treated similarly.
With this procedure, the engsln.XX outputs are obtained from a small number of MD frames.

The soln/MDinfo file then reads

(number of frames) 2
100 900
9 3

and the necessary force-field inputs are only SltInfo and MolPrm2.
In the present example, EtOH is the first species of the mixed solvent, and its force-field parameters are stored in MolPrm1 in the usual setup.
When the number of solute molecules is larger than 1, though, MolPrm1 is the same as SltInfo and is not necessary.
MolPrm2 is necessary since it has the force-field parameters of water.

Similarly, when the water molecules is the solute, ermod performs 900 samplings of solute-solvent configuration for a single snapshot of the soln system given above.
The necessary force-field inputs are then SltInfo and MolPrm1.
MolPrm1 corresponds to EtOH. MolPrm2 is for water and is the same as SltInfo when water is the solute.

The refs calculation is conducted just as in the case of a single solute molecule.
Indeed, the number of inserted particles is always 1.
The refs/MDinfo file is then

(number of frames) 2
99 900
9 3

when the solute is EtOH, and it is

(number of frames) 2
100 899
9 3

when the solute is water.