Recent changes to TooLargeMinimum

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 29 Apr 2024 03:09:10 -0000

--- v15
+++ v16
@@ -1,4 +1,4 @@
-Error in running ermod: The minimum of the energy coordinate is too large
+Error in running erdst: The minimum of the energy coordinate is too large
 ====

 The solute-solvent pair energy is meshed for constructing distribution functions.
@@ -6,7 +6,7 @@
 The above error message shows that the smallest-energy mesh stays at too high-energy region compared to the minimum possible value of the solute-solvent pair interaction.
 This error may happen when the solute is highly charged, in particular.

-If user sees the above error only in the ermod run for the reference solvent (not for the solution run),
+If user sees the above error only in the erdst run for the reference solvent (not for the solution run),
 the single-molecule simulation of the isolate solute can be a source of the problem.
 See also [Practices for a single-molecule simulation of isolated solute](single-solute).

@@ -17,7 +17,7 @@
 One is to use an option in the gen_input script, and the other is to open and edit the parameters_er file.
 In both schemes, the effect is that the the ecdmin parameter within the parameters_er file is modified.

-When user modifies ecdmin, he needs to run the ermod program again.
+When user modifies ecdmin, he needs to run the erdst 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.
@@ -81,7 +81,7 @@
 ~~~~

 the first column in the first line shows that the trajectory of the solution system  contains 10000 frames.
-A short ermod run can be performed simply by changing this entry, for example,  into 50.
+A short erdst run can be performed simply by changing this entry, for example,  into 50.
 With this, only 50 frames from the 10000 are read by the ermod program.
 In the short ermod run of the solution system to obtain uvrange.tt, it is advised to set "engdiv = 1" in parameters_er.
 It is further advised to set ecdmin very small, for example, to -500.

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 03 Oct 2019 08:44:46 -0000

--- v14
+++ v15
@@ -34,7 +34,7 @@
 The two scheme are equivalent.
 The option of --minenergy _energy_ within the gen_input script is actually to re-write the the ecdmin parameter in parameters_er.

-It is warned that when ecdmin is unnecessary small, the output files of engsln.XX, engref.XX, and corref.XX will be large in size.
+It is warned that when ecdmin is unnecessarily small, the output files of engsln.XX, engref.XX, and corref.XX will be large in size.
 This makes the slvfe run slow.
 It is usually enough to take ecdmin to be smaller by a few kcal/mol than the minimum possible energy between solute and solvent

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 03 Oct 2019 08:43:05 -0000

--- v13
+++ v14
@@ -22,9 +22,7 @@
 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.

-The first scheme uses the gen_input script and is available at the moment for ver 0.2.x of ERmod with gromacs and for ver 0.3.x of ERmod with gromacs or AMBER.
-This scheme is not ready yet for NAMD.
-The scheme is to pass the option of --minenergy _energy_ to gen_input to modify the minimum mesh energy from the default value of -20.0 kca/mol.
+The first scheme is to pass the option of --minenergy _energy_ to gen_input to modify the minimum mesh energy from the default value of -20.0 kca/mol.
 The _energy_ value should be chosen to be small enough.
 A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
 When the charge is +/-2, --minenergy -120 will be a good starting point.
@@ -35,6 +33,10 @@

 The two scheme are equivalent.
 The option of --minenergy _energy_ within the gen_input script is actually to re-write the the ecdmin parameter in parameters_er.
+
+It is warned that when ecdmin is unnecessary small, the output files of engsln.XX, engref.XX, and corref.XX will be large in size.
+This makes the slvfe run slow.
+It is usually enough to take ecdmin to be smaller by a few kcal/mol than the minimum possible energy between solute and solvent

 With the 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.

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 12 Nov 2018 09:34:48 -0000

--- v12
+++ v13
@@ -22,7 +22,7 @@
 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.

-The first scheme uses the gen_input script and is available at the moment for ver 0.2.x of ERMOD with gromacs and for ver 0.3.x of ERMOD with gromacs or AMBER.
+The first scheme uses the gen_input script and is available at the moment for ver 0.2.x of ERmod with gromacs and for ver 0.3.x of ERmod with gromacs or AMBER.
 This scheme is not ready yet for NAMD.
 The scheme is to pass the option of --minenergy _energy_ to gen_input to modify the minimum mesh energy from the default value of -20.0 kca/mol.
 The _energy_ value should be chosen to be small enough.

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 12 Nov 2018 09:32:33 -0000

--- v11
+++ v12
@@ -6,7 +6,7 @@
 The above error message shows that the smallest-energy mesh stays at too high-energy region compared to the minimum possible value of the solute-solvent pair interaction.
 This error may happen when the solute is highly charged, in particular.

-If user sees the above error in the ermod run for the reference solvent,
+If user sees the above error only in the ermod run for the reference solvent (not for the solution run),
 the single-molecule simulation of the isolate solute can be a source of the problem.
 See also [Practices for a single-molecule simulation of isolated solute](single-solute).

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 26 Jun 2018 01:49:51 -0000

--- v10
+++ v11
@@ -5,6 +5,10 @@
 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 the minimum possible value of the solute-solvent pair interaction.
 This error may happen when the solute is highly charged, in particular.
+
+If user sees the above error in the ermod run for the reference solvent,
+the single-molecule simulation of the isolate solute can be a source of the problem.
+See also [Practices for a single-molecule simulation of isolated solute](single-solute).

 When user encounters the problem of minimum energy coordinate, the smallest-energy mesh needs to be shifted to further smaller-energy region.
 The coordinate value of the smallest-energy mesh is called ecdmin, which is stored in the parameters_er file.

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 08 May 2015 05:53:56 -0000

--- v9
+++ v10
@@ -24,7 +24,7 @@
 The _energy_ value should be chosen to be small enough.
 A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
 When the charge is +/-2, --minenergy -120 will be a good starting point.
-For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).
+For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameter files for ermod](parameters-ermod03).

 The second scheme is more versatile.
 User opens the parameters_er file and directly modifies the ecdmin parameter in it.
@@ -35,7 +35,7 @@
 With the 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 (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).
+The parameters contained in the parameters_er file are described in [Parameter files for ermod](parameters-ermod03).

 uvrange.tt can be helpful when user wants to estimate the minimum energy.
 This file is generated when the ermod program finishes successfully.

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 03 Mar 2014 03:31:42 -0000

--- v8
+++ v9
@@ -44,15 +44,24 @@
 ~~~~
  species     minimum        maximum
     0       -0.08086        0.00799
-    1      -30.66799       0.65871E+34
-    2      -13.02511       0.79338E+38
+    1      -30.66799       14.66573
+    2       -7.40580        5.36599
 ~~~~

-In this list, the species 0 corresponds to the self-enegy of the solute. Shown are the minimum and maximum of the solute self-energy.
+In this list, the species 0 corresponds to the self-enegy of the solute.
+Shown are the minimum and maximum of the solute self-energy.
 The self-energy is usually small in magnitude when a large MD unit cell is used.
-The species 1 is the 1st solvent species, and the minimum and maximum of the pair energy between the solute and the 1st solvent species are shown.
+The species 1 is the 1st solvent species,
+and the minimum and maximum of the pair energy between the solute and the 1st solvent species are shown.
 Similarly for the species 2, and so on.
-In this example, the minimum pair energy of the solute is -30.7 kcal/mol against the solvent  species 1 and is -13.0 kcal/mol against the solvent species 2.
+In this example, the minimum pair energy of the solute is -30.7 kcal/mol against the solvent species 1 and is -7.4 kcal/mol against the solvent species 2.
+
+The above example is for the solution system.
+When the system is the reference solvent, the value of the maximum energy will be very large.
+The solute is inserted into the reference solvent as a test particle,
+and the overlap of solute and solvent is allowed.
+The pair energy is very large at overlap,
+and this is reflected in a large maximum observed in uvrange.tt of reference solvent.

 When user encounters the above error message, he is advised to conduct a short run of ermod of the solution system.
 A simple scheme to do so is to modify the MDinfo file for the moment.

TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 31 Oct 2013 01:32:10 -0000

--- v7
+++ v8
@@ -24,7 +24,7 @@
 The _energy_ value should be chosen to be small enough.
 A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
 When the charge is +/-2, --minenergy -120 will be a good starting point.
-For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameters for ermod](parameters-ermod)).
+For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).

 The second scheme is more versatile.
 User opens the parameters_er file and directly modifies the ecdmin parameter in it.
@@ -35,7 +35,7 @@
 With the 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).
+The parameters contained in the parameters_er file are described in [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).

 uvrange.tt can be helpful when user wants to estimate the minimum energy.
 This file is generated when the ermod program finishes successfully.

WikiPage TooLargeMinimum modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 06 May 2012 13:41:01 -0000

--- v6 
+++ v7 
@@ -7,28 +7,35 @@
 This error may happen when the solute is highly charged, in particular.
 
 When user encounters the problem of minimum energy coordinate, the smallest-energy mesh needs to be shifted to further smaller-energy region.
-To cure the problem, user opens the parameters_er file and modifies the ecdmin parameter in it.
+The coordinate value of the smallest-energy mesh is called ecdmin, which is stored in the parameters_er file.
 The default value of ecdmin is -20.0e0 (kcal/mol), so that user makes the value smaller, for example, to -25.0e0.
+There are two schemes to (re-)set the ecdmin value and cure the problem.
+One is to use an option in the gen_input script, and the other is to open and edit the parameters_er file.
+In both schemes, the effect is that the the ecdmin parameter within the parameters_er file is modified.
+
 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.
-
-There is another scheme using the gen_input script if user uses ver 0.2.x of ERMOD with gromacs or uses ver 0.3.x of ERMOD with gromacs or AMBER.
-The following scheme using gen_input is not ready for NAMD.
+The first scheme uses the gen_input script and is available at the moment for ver 0.2.x of ERMOD with gromacs and for ver 0.3.x of ERMOD with gromacs or AMBER.
+This scheme is not ready yet for NAMD.
 The scheme is to pass the option of --minenergy _energy_ to gen_input to modify the minimum mesh energy from the default value of -20.0 kca/mol.
-The _energy_ value should be chosen so that it is small enough.
+The _energy_ value should be chosen to be small enough.
 A general guideline is that for an ion of total charge of +/-1, --minenergy -80 will be a good starting point.
 When the charge is +/-2, --minenergy -120 will be a good starting point.
 For an ion with extreme charge, user should use the EcdInfo file (see the EcdInfo section of [Parameters for ermod](parameters-ermod)).
-Actually, the scheme of using the option of --minenergy _energy_ in the gen_input script is equivalent to changing the ecdmin parameter in parameters_er.
+
+The second scheme is more versatile.
+User opens the parameters_er file and directly modifies the ecdmin parameter in it.
+
+The two scheme are equivalent.
+The option of --minenergy _energy_ within the gen_input script is actually to re-write the the ecdmin parameter in parameters_er.
+
+With the 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).
-
 
 uvrange.tt can be helpful when user wants to estimate the minimum energy.
 This file is generated when the ermod program finishes successfully.