Recent changes to ErrorMessages

ErrorMessages modified by Logan Abbott

Logan Abbott — Sun, 01 Dec 2024 14:56:54 -0000

WikiPage ErrorMessages modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 21 Apr 2012 05:30:24 -0000

--- v5 
+++ v6 
@@ -1,52 +1,0 @@
-Common Error and Warning Messages which are Often Resolved Easily
-====
-
-The minimum of the energy coordinate is too large
-----
-The solute-solvent pair energy is meshed for constructing distribution functions.
-The smallest one of the meshed energies needs to be more negative than the minimum possible energy between solute and solvent; otherwise some energy values cannot be thrown into any mesh.
-The above error message shows that the smallest-energy mesh stays at too high-energy region compared to minimum possible value of the solute-solvent pair interaction.
-In this case, the smallest-energy mesh needs to be shifted to further smaller-energy region.
-
-To do so, user opens the parameters_er file and modify the ecdmin parameter in it.
-The default value of ecdmin is -20.0e0 (kcal/mol), so that user makes the value smaller, for example, to -25.0e0.
-When user modifies ecdmin, he needs to run the ermod program again.
-If he encounters the same error message, ecdmin needs to be further smaller.
-
-The energy meshes must be identical between soln and refs.
-Thus, when user changes the ecdmin parameter, he has to do so both for soln/parameters_er and refs/parameters_er.
-
-With the above modification, ecdmin may become unphysically small.
-In this case, there is likely to be some mistake or inconsistency in the MD setup and a system-specific treatment will be required.
-
-The parameters contained in the parameters_er file are described in [Parameter files for ermod](parameters-ermod).
-
-
-Incorrect normalization at (number specifying the solvent species)
-----
-The number of solvent molecules needs to be the same between soln and refs.
-When the system is of mixed solvent, the number is identical for each solvent species.
-The number of solvent molecules is counted from soln/engsln.xx and refs/engref.xx, where xx is a two-digit integer.
-In principle, the number from engsln is coincident to the number from engref.
-Due to the finite-digit representation of numbers on computer, however, the two numbers can be different.
-The slvfe program runs successfully only when the difference is within a certain allowance, and it terminates with the above error message when the difference is larger than that allowance.
-The allowance has a parameter name of tiny, and can be modified in the parameters_fe file.
-The default value of tiny is 1.0e-10, and the error message shows that the allowance is too stringent.
-
-When user sees the above error message, he opens the parameters_fe file and make tiny larger.
-For example, he may increase it to 1.0e-9.
-When user modifies tiny, he needs to run the slvfe program again.
-If he encounters the same error message, tiny needs to be further larger.
-
-If user needs too large tiny to make slvfe run (for example, 1.0e-1), there is likely some inconsistency in the system setup.
-The numbers of solvent molecules in soln and refs are both integers.
-In numerical realization, they are calculated from soln/engsln and refs/engref first as real and are converted into integer.
-A too large difference should not be there between the two numbers even in the numerical process; it is an indication of some mistake or inconsistency of solvent specification.
-
-The parameters contained in the parameters_fe file are described in [Parameter files for slvfe](parameters-slvfe).
-
-
-Warning: mesh error is (value1) kcal/mol and is larger than the recommended value of (value2) kcal/mol
-----
-
-The parameters contained in the parameters_fe file are described in [Parameter files for slvfe](parameters-slvfe).

WikiPage ErrorMessages modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 21 Apr 2012 04:33:38 -0000

--- v4 
+++ v5 
@@ -44,3 +44,9 @@
 A too large difference should not be there between the two numbers even in the numerical process; it is an indication of some mistake or inconsistency of solvent specification.
 
 The parameters contained in the parameters_fe file are described in [Parameter files for slvfe](parameters-slvfe).
+
+
+Warning: mesh error is (value1) kcal/mol and is larger than the recommended value of (value2) kcal/mol
+----
+
+The parameters contained in the parameters_fe file are described in [Parameter files for slvfe](parameters-slvfe).

WikiPage ErrorMessages modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 21 Apr 2012 04:14:03 -0000

--- v3 
+++ v4 
@@ -1,46 +1,46 @@
-Common Error Messages which are Often Resolved Easily
+Common Error and Warning Messages which are Often Resolved Easily
 ====
 
 The minimum of the energy coordinate is too large
 ----
 The solute-solvent pair energy is meshed for constructing distribution functions.
 The smallest one of the meshed energies needs to be more negative than the minimum possible energy between solute and solvent; otherwise some energy values cannot be thrown into any mesh.
 The above error message shows that the smallest-energy mesh stays at too high-energy region compared to minimum possible value of the solute-solvent pair interaction.
 In this case, the smallest-energy mesh needs to be shifted to further smaller-energy region.
 
 To do so, user opens the parameters_er file and modify the ecdmin parameter in it.
 The default value of ecdmin is -20.0e0 (kcal/mol), so that user makes the value smaller, for example, to -25.0e0.
 When user modifies ecdmin, he needs to run the ermod program again.
 If he encounters the same error message, ecdmin needs to be further smaller.
 
 The energy meshes must be identical between soln and refs.
 Thus, when user changes the ecdmin parameter, he has to do so both for soln/parameters_er and refs/parameters_er.
 
 With the above modification, ecdmin may become unphysically small.
 In this case, there is likely to be some mistake or inconsistency in the MD setup and a system-specific treatment will be required.
 
 The parameters contained in the parameters_er file are described in [Parameter files for ermod](parameters-ermod).
 
 
 Incorrect normalization at (number specifying the solvent species)
 ----
 The number of solvent molecules needs to be the same between soln and refs.
 When the system is of mixed solvent, the number is identical for each solvent species.
 The number of solvent molecules is counted from soln/engsln.xx and refs/engref.xx, where xx is a two-digit integer.
 In principle, the number from engsln is coincident to the number from engref.
 Due to the finite-digit representation of numbers on computer, however, the two numbers can be different.
 The slvfe program runs successfully only when the difference is within a certain allowance, and it terminates with the above error message when the difference is larger than that allowance.
 The allowance has a parameter name of tiny, and can be modified in the parameters_fe file.
 The default value of tiny is 1.0e-10, and the error message shows that the allowance is too stringent.
 
 When user sees the above error message, he opens the parameters_fe file and make tiny larger.
 For example, he may increase it to 1.0e-9.
 When user modifies tiny, he needs to run the slvfe program again.
 If he encounters the same error message, tiny needs to be further larger.
 
 If user needs too large tiny to make slvfe run (for example, 1.0e-1), there is likely some inconsistency in the system setup.
 The numbers of solvent molecules in soln and refs are both integers.
 In numerical realization, they are calculated from soln/engsln and refs/engref first as real and are converted into integer.
 A too large difference should not be there between the two numbers even in the numerical process; it is an indication of some mistake or inconsistency of solvent specification.
 
-The parameters contained in the parameters_er file are described in [Parameter files for slvfe](parameters-slvfe).
+The parameters contained in the parameters_fe file are described in [Parameter files for slvfe](parameters-slvfe).

WikiPage ErrorMessages modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 19 Apr 2012 10:18:17 -0000

--- v2 
+++ v3 
@@ -38,9 +38,6 @@
 When user modifies tiny, he needs to run the slvfe program again.
 If he encounters the same error message, tiny needs to be further larger.
 
-When user changes the tiny value and runs the slvfe program successfully, it is advised that he further modify tiny, for example, successively from 1.0e-9 to 1.0e-5 and see the change in the solvation free energy calculated.
-Typically he will see no change in the free energy output.
-
 If user needs too large tiny to make slvfe run (for example, 1.0e-1), there is likely some inconsistency in the system setup.
 The numbers of solvent molecules in soln and refs are both integers.
 In numerical realization, they are calculated from soln/engsln and refs/engref first as real and are converted into integer.

WikiPage ErrorMessages modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 19 Apr 2012 07:16:51 -0000

--- v1 
+++ v2 
@@ -1,4 +1,4 @@
-Common Error Messages Which are Often Resolved Easily
+Common Error Messages which are Often Resolved Easily
 ====
 
 The minimum of the energy coordinate is too large

WikiPage ErrorMessages modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 19 Apr 2012 07:15:29 -0000

Common Error Messages Which are Often Resolved Easily ==== The minimum of the energy coordinate is too large ---- The solute-solvent pair energy is meshed for constructing distribution functions. The smallest one of the meshed energies needs to be more negative than the minimum possible energy between solute and solvent; otherwise some energy values cannot be thrown into any mesh. The above error message shows that the smallest-energy mesh stays at too high-energy region compared to minimum possible value of the solute-solvent pair interaction. In this case, the smallest-energy mesh needs to be shifted to further smaller-energy region. To do so, user opens the parameters_er file and modify the ecdmin parameter in it. The default value of ecdmin is -20.0e0 (kcal/mol), so that user makes the value smaller, for example, to -25.0e0. When user modifies ecdmin, he needs to run the ermod program again. If he encounters the same error message, ecdmin needs to be further smaller. The energy meshes must be identical between soln and refs. Thus, when user changes the ecdmin parameter, he has to do so both for soln/parameters_er and refs/parameters_er. With the above modification, ecdmin may become unphysically small. In this case, there is likely to be some mistake or inconsistency in the MD setup and a system-specific treatment will be required. The parameters contained in the parameters_er file are described in [Parameter files for ermod](parameters-ermod). Incorrect normalization at (number specifying the solvent species) ---- The number of solvent molecules needs to be the same between soln and refs. When the system is of mixed solvent, the number is identical for each solvent species. The number of solvent molecules is counted from soln/engsln.xx and refs/engref.xx, where xx is a two-digit integer. In principle, the number from engsln is coincident to the number from engref. Due to the finite-digit representation of numbers on computer, however, the two numbers can be different. The slvfe program runs successfully only when the difference is within a certain allowance, and it terminates with the above error message when the difference is larger than that allowance. The allowance has a parameter name of tiny, and can be modified in the parameters_fe file. The default value of tiny is 1.0e-10, and the error message shows that the allowance is too stringent. When user sees the above error message, he opens the parameters_fe file and make tiny larger. For example, he may increase it to 1.0e-9. When user modifies tiny, he needs to run the slvfe program again. If he encounters the same error message, tiny needs to be further larger. When user changes the tiny value and runs the slvfe program successfully, it is advised that he further modify tiny, for example, successively from 1.0e-9 to 1.0e-5 and see the change in the solvation free energy calculated. Typically he will see no change in the free energy output. If user needs too large tiny to make slvfe run (for example, 1.0e-1), there is likely some inconsistency in the system setup. The numbers of solvent molecules in soln and refs are both integers. In numerical realization, they are calculated from soln/engsln and refs/engref first as real and are converted into integer. A too large difference should not be there between the two numbers even in the numerical process; it is an indication of some mistake or inconsistency of solvent specification. The parameters contained in the parameters_er file are described in [Parameter files for slvfe](parameters-slvfe).