Recent changes to QuickStartGuide-LAMMPS

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 25 Jul 2025 04:34:41 -0000

--- v28
+++ v29
@@ -1,6 +1,6 @@
 Quick Start Guide: LAMMPS
 ====
-Generate input configuration for running erdst
+Generate input configuration for solvation free energy calculation
 ----
 Input configuration file for erdst and slvfe will be generated via helper scripts.
 First, execute the following command to generate system information:

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 23 Dec 2024 10:21:52 -0000

--- v27
+++ v28
@@ -53,12 +53,12 @@
 (ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --log ../solution.log --input ../solution.in
 ~~~~

-The trajectory (xtc file) and log and input files are fed to the script.
+The trajectory file (.xtc), the log file of MD (.log), and the LAMMPS input script (.in) are fed to the script.
 The options --traj, --log, and --input can be simplified to -t, -l, and -i, respectively. 
 After running the script, a symbolic link file, namely HISTORY, is to be created.
 A file named parameters_er is also to be created; this file controls how the erdst program runs.
 MDinfo is further to be updated; “FRAME” on the first line is replaced by the number of snapshots in trajectory.
-Between the log and input files, the information within the log file is of higher priority.
+Between the .log and .in files, the information within the former is of higher priority.

 Start the solute-solvent interaction calculation in the solution system with:

@@ -82,7 +82,7 @@
 (ERmod directory)/bin/erdst
 ~~~~

-The first three arguments are to be taken similarly to the case of the solution (of course, the xtc, log, and input files are changed to those of the solvent system without solute). The fourth argument, --flexible, specifies that the test-particle insertion calculation is performed with flexible structures of the solute.
+The first three arguments are to be taken similarly to the case of the solution (of course, the .xtc, .log, and .in files are changed to those of the solvent system without solute). The fourth argument, --flexible, specifies that the test-particle insertion calculation is performed with flexible structures of the solute.
 The option --flexible can be simplified to -s.
 In addition to a symbolic link named HISTORY, a symbolic link file named SltConf is generated; HISTORY refers to the trajectory of the solvent, solvent.xtc, and SltConf is linked to the trajectory file of the isolated solute, solute.xtc.

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 23 Dec 2024 08:07:42 -0000

--- v26
+++ v27
@@ -50,27 +50,15 @@

 ~~~~
 cd soln
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --log ../solution.log
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --log ../solution.log --input ../solution.in
 ~~~~

-The trajectory (xtc file) and log files are fed to the script.
-The options --traj and --log can be simplified to -t and -l, respectively. 
+The trajectory (xtc file) and log and input files are fed to the script.
+The options --traj, --log, and --input can be simplified to -t, -l, and -i, respectively. 
 After running the script, a symbolic link file, namely HISTORY, is to be created.
 A file named parameters_er is also to be created; this file controls how the erdst program runs.
 MDinfo is further to be updated; “FRAME” on the first line is replaced by the number of snapshots in trajectory.
-
-In some cases, the information in the log file that is specfied with the --log option of gen_input is not sufficient to construct a parameters_er file.
-gen_input is then to be executed also with an opion of --input, which takes an LAMMPS input script for MD.
-An example is
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --input ../solution.in
-~~~~
-If this still does not work, gen_input will work with
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --log ../solution.log --input ../solution.in
-~~~~
-When both of the log file and the input script are fed to gen_input, the information within the log file is adopted.
-The option --input can be simplified to -i.
+Between the log and input files, the information within the log file is of higher priority.

 Start the solute-solvent interaction calculation in the solution system with:

@@ -90,23 +78,13 @@

 ~~~~
 cd ../refs
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --flexible ../solute.xtc
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --input ../solvent.in --flexible ../solute.xtc
 (ERmod directory)/bin/erdst
 ~~~~

-The first two arguments are to be taken similarly to the case of the solution (of course, the xtc and log files are changed to those of the solvent system without solute).
-The third argument, --flexible, specifies that the test-particle insertion calculation is performed with flexible structures of the solute.
+The first three arguments are to be taken similarly to the case of the solution (of course, the xtc, log, and input files are changed to those of the solvent system without solute). The fourth argument, --flexible, specifies that the test-particle insertion calculation is performed with flexible structures of the solute.
 The option --flexible can be simplified to -s.
 In addition to a symbolic link named HISTORY, a symbolic link file named SltConf is generated; HISTORY refers to the trajectory of the solvent, solvent.xtc, and SltConf is linked to the trajectory file of the isolated solute, solute.xtc.
-
-If gen_input fails with the above, it will work with
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --input ../solvent.in --flexible ../solute.xtc
-~~~~
-or
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --input ../solvent.in --flexible ../solute.xtc
-~~~~

 After running erdst, user obtains the energy distributions for the insertion operation.
 engref.xx is the histogram of the solute-solvent pair interaction energy at insertions in reference system, and corref.xx is the correlation matrix.
@@ -132,25 +110,16 @@

 ~~~~
 cd ../refs
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --rigid ../solute.data
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --input ../solvent.in --rigid ../solute.data
 (ERmod directory)/bin/erdst
 ~~~~

-The difference from the flexible solute case is the third argument.
-The third argument, --rigid, specifies that the test-particle insertion calculation is performed with fixed structure of the solute.
+The difference from the flexible solute case is the fourth argument.
+The fourth argument, --rigid, specifies that the test-particle insertion calculation is performed with fixed structure of the solute.
 The option --rigid can be simplified to -r.
 The structure of the solute is taken from the SltInfo file when the solute is rigid.
 See [Parameter files for erdst](parameters-erdst) for the format of the SltInfo file in the case of rigid solute.
 When the refs calculation is done, the calculation of solvation free energy of rigid solute can be done with the same procedure as that in the flexible case.
-
-If gen_input fails with the above, it will work with
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --input ../solvent.in --rigid ../solute.data
-~~~~
-or
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --input ../solvent.in --rigid ../solute.data
-~~~~

 The option of --help or -h shows the help message for gen_structure and gen_input.

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 20 Dec 2024 08:53:17 -0000

--- v25
+++ v26
@@ -29,16 +29,16 @@

 ~~~~
 FRAME 2
-1 1000
+1 500
 9 3
 ~~~~

 The second column of the first line indicates that there are 2 types of molecular species.
-The second line states that the system contains 1 molecule of C2H6O type and 1000 molecules of H2O type (C2H6O and H2O are the molecular types in the topology file).
+The second line states that the system contains 1 molecule of C2H6O type and 500 molecules of H2O type (C2H6O and H2O are the molecular types in the topology file).
 The last line states that 9 atoms are present within a single C2H6O molecule and that 3 atoms are present within a single H2O molecule.

 In the reference system (refs directory,) MDinfo file is also generated.
-But the number of molecular species in refs/MDinfo is smaller by 1 that that in soln/MDinfo, since refs/MDinfo carries only the information of the solvent system without solute.
+But the number of molecular species in refs/MDinfo is smaller by 1 than that in soln/MDinfo, since refs/MDinfo carries only the information of the solvent system without solute.

 Both in soln and refs directories, MolPrmX  (X = 1, 2, ...) and SltInfo should be found.
 MolPrmX is the parameter file for solvent species, and SltInfo is the parameter file for solute.

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 20 Dec 2024 06:18:30 -0000

--- v24
+++ v25
@@ -65,7 +65,7 @@
 ~~~~
 (ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --input ../solution.in
 ~~~~
-If this still does not work, gen_input works witj
+If this still does not work, gen_input will work with
 ~~~~
 (ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --log ../solution.log --input ../solution.in
 ~~~~

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 20 Dec 2024 06:09:52 -0000

--- v23
+++ v24
@@ -59,6 +59,19 @@
 A file named parameters_er is also to be created; this file controls how the erdst program runs.
 MDinfo is further to be updated; “FRAME” on the first line is replaced by the number of snapshots in trajectory.

+In some cases, the information in the log file that is specfied with the --log option of gen_input is not sufficient to construct a parameters_er file.
+gen_input is then to be executed also with an opion of --input, which takes an LAMMPS input script for MD.
+An example is
+~~~~
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --input ../solution.in
+~~~~
+If this still does not work, gen_input works witj
+~~~~
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --log ../solution.log --input ../solution.in
+~~~~
+When both of the log file and the input script are fed to gen_input, the information within the log file is adopted.
+The option --input can be simplified to -i.
+
 Start the solute-solvent interaction calculation in the solution system with:

 ~~~~
@@ -85,6 +98,15 @@
 The third argument, --flexible, specifies that the test-particle insertion calculation is performed with flexible structures of the solute.
 The option --flexible can be simplified to -s.
 In addition to a symbolic link named HISTORY, a symbolic link file named SltConf is generated; HISTORY refers to the trajectory of the solvent, solvent.xtc, and SltConf is linked to the trajectory file of the isolated solute, solute.xtc.
+
+If gen_input fails with the above, it will work with
+~~~~
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --input ../solvent.in --flexible ../solute.xtc
+~~~~
+or
+~~~~
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --input ../solvent.in --flexible ../solute.xtc
+~~~~

 After running erdst, user obtains the energy distributions for the insertion operation.
 engref.xx is the histogram of the solute-solvent pair interaction energy at insertions in reference system, and corref.xx is the correlation matrix.
@@ -121,14 +143,16 @@
 See [Parameter files for erdst](parameters-erdst) for the format of the SltInfo file in the case of rigid solute.
 When the refs calculation is done, the calculation of solvation free energy of rigid solute can be done with the same procedure as that in the flexible case.

+If gen_input fails with the above, it will work with
+~~~~
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --input ../solvent.in --rigid ../solute.data
+~~~~
+or
+~~~~
+(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --input ../solvent.in --rigid ../solute.data
+~~~~
+
 The option of --help or -h shows the help message for gen_structure and gen_input.
-In some cases, the information in the log file that is specfied with the --log option of gen_input is not sufficient to construct a parameters_er file.
-gen_input is then to be executed also with an opion of --input, which takes an LAMMPS input script for MD.
-An example is
-~~~~
-(ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solution.xtc --input ../solution.in
-~~~~
-When both of the log file and the input script are fed to gen_input, the information within the log file is adopted.

 At the moment, gen_input cannot read parameters from variable  in the LAMMPS input script for
 ~~~~

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 02:18:27 -0000

--- v22
+++ v23
@@ -2,7 +2,7 @@
 ====
 Generate input configuration for running erdst
 ----
-Input configuration file for ermod and slvfe will be generated via helper scripts.
+Input configuration file for erdst and slvfe will be generated via helper scripts.
 First, execute the following command to generate system information:

 ~~~~
@@ -98,7 +98,7 @@

 The trajectory is divided into a set of blocks both for soln and refs.
 The default value of the number of divisions is 10 for the solution system and is 5 for the reference.
-The number of divisions can be modified with the numdiv parameter in the parameters_er file when the ermod program is run.
+The number of divisions can be modified with the numdiv parameter in the parameters_er file when the erdst program is run.
 See [Parameter files for erdst](parameters-erdst) for the description of the parameters which can be specified in parameters_er.

 If the solute is rigid (its intramolecular structure is fixed), the procedure is simplified.

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 02:17:19 -0000

--- v21
+++ v22
@@ -1,6 +1,6 @@
 Quick Start Guide: LAMMPS
 ====
-Generate input configuration for running ermod
+Generate input configuration for running erdst
 ----
 Input configuration file for ermod and slvfe will be generated via helper scripts.
 First, execute the following command to generate system information:
@@ -23,7 +23,7 @@
 After the execution, two directories are created, namely soln and refs.
 The soln directory has `MDinfo`, `MolPrmX` (X = 1, 2, ...) , `SltInfo`, and `.extraparam`,
 and the refs directory has `MDinfo`, `MolPrmX` (X = 1, 2, ...) , and `SltInfo`.
-See [Parameter files for ermod](parameters-ermod03) for detailed description of SltInfo, MolPrm1, and so on.
+See [Parameter files for erdst](parameters-erdst) for detailed description of SltInfo, MolPrm1, and so on.

 soln/MDinfo should read, for example, as

@@ -56,7 +56,7 @@
 The trajectory (xtc file) and log files are fed to the script.
 The options --traj and --log can be simplified to -t and -l, respectively. 
 After running the script, a symbolic link file, namely HISTORY, is to be created.
-A file named parameters_er is also to be created; this file controls how the ermod program runs.
+A file named parameters_er is also to be created; this file controls how the erdst program runs.
 MDinfo is further to be updated; “FRAME” on the first line is replaced by the number of snapshots in trajectory.

 Start the solute-solvent interaction calculation in the solution system with:

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 02:16:03 -0000

--- v20
+++ v21
@@ -43,7 +43,7 @@
 Both in soln and refs directories, MolPrmX  (X = 1, 2, ...) and SltInfo should be found.
 MolPrmX is the parameter file for solvent species, and SltInfo is the parameter file for solute.
 Both files contain the Lennard-Jones parameters and charge information, which are necessary in the calculation.
-See [Parameter files for ermod](parameters-ermod03) for detailed description of MDInfo, SltInfo, MolPrmX, and so on.
+See [Parameter files for erdst](parameters-erdst) for detailed description of MDInfo, SltInfo, MolPrmX, and so on.

 Now the parameters for the solution system are prepared.
 Move to soln directory and run the helper script:
@@ -99,7 +99,7 @@
 The trajectory is divided into a set of blocks both for soln and refs.
 The default value of the number of divisions is 10 for the solution system and is 5 for the reference.
 The number of divisions can be modified with the numdiv parameter in the parameters_er file when the ermod program is run.
-See [Parameter files for ermod](parameters-ermod03) for the description of the parameters which can be specified in parameters_er.
+See [Parameter files for erdst](parameters-erdst) for the description of the parameters which can be specified in parameters_er.

 If the solute is rigid (its intramolecular structure is fixed), the procedure is simplified.
 The scheme for the solution part is the same as above.
@@ -118,7 +118,7 @@
 The third argument, --rigid, specifies that the test-particle insertion calculation is performed with fixed structure of the solute.
 The option --rigid can be simplified to -r.
 The structure of the solute is taken from the SltInfo file when the solute is rigid.
-See [Parameter files for ermod](parameters-ermod03) for the format of the SltInfo file in the case of rigid solute.
+See [Parameter files for erdst](parameters-erdst) for the format of the SltInfo file in the case of rigid solute.
 When the refs calculation is done, the calculation of solvation free energy of rigid solute can be done with the same procedure as that in the flexible case.

 The option of --help or -h shows the help message for gen_structure and gen_input.

QuickStartGuide-LAMMPS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Mon, 09 Dec 2024 02:14:34 -0000

--- v19
+++ v20
@@ -84,16 +84,16 @@
 The first two arguments are to be taken similarly to the case of the solution (of course, the xtc and log files are changed to those of the solvent system without solute).
 The third argument, --flexible, specifies that the test-particle insertion calculation is performed with flexible structures of the solute.
 The option --flexible can be simplified to -s.
-In addition to a symbolic link named HISTORY, a symbolic link file named SltConf is generated; HISTORY refers to the trajectory of the solvent, solvent_run.xtc, and SltConf is linked to the trajectory file of the isolated solute, solute_run.xtc.
+In addition to a symbolic link named HISTORY, a symbolic link file named SltConf is generated; HISTORY refers to the trajectory of the solvent, solvent.xtc, and SltConf is linked to the trajectory file of the isolated solute, solute.xtc.

-After running ermod, user obtains the energy distributions for the insertion operation.
+After running erdst, user obtains the energy distributions for the insertion operation.
 engref.xx is the histogram of the solute-solvent pair interaction energy at insertions in reference system, and corref.xx is the correlation matrix.
 The two-digit numbers indicate which fraction of the trajectory the file corresponds to.
 For example, the trajectory is divided into 5 blocks.
 engref.01 and corref.01 are then obtained from the first one of the 5 blocks, and engref.02 and corref.02 are from the second one.
 Correspondingly, the output distribution functions are obtained from each of the 5 blocks.

-When two ermod runs are finished in the soln and refs directories, the solvation free energy can be calculated from the distribution functions obtained.
+When two erdst runs are finished in the soln and refs directories, the solvation free energy can be calculated from the distribution functions obtained.
 Go to [Quick Start Guide](QuickStartGuide) ---- Running slvfe: Getting Final Output.

 The trajectory is divided into a set of blocks both for soln and refs.
@@ -111,7 +111,7 @@
 ~~~~
 cd ../refs
 (ERmod directory)/share/ermod/tools/LAMMPS/gen_input --traj ../solvent.xtc --log ../solvent.log --rigid ../solute.data
-(ERmod directory)/bin/ermod
+(ERmod directory)/bin/erdst
 ~~~~

 The difference from the flexible solute case is the third argument.