Recent changes to QuickStartGuide-GROMACS

QuickStartGuide-GROMACS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 23 Dec 2025 03:55:23 -0000

--- v65
+++ v66
@@ -141,7 +141,7 @@
 Both in soln and refs directories, MolPrm1 and SltInfo should be found.
 MolPrm1 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  (X = 1, 2, ...), and so on.
+See [Parameter files for erdst](parameters-erdst) for detailed description of MDInfo, SltInfo, MolPrmX  (X = 1, 2, ...), and so on.

 Now the parameters for the solution system are prepared.
 Move to soln directory and run the helper script:
@@ -199,7 +199,7 @@
 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 erdst program is run.
-See [Parameter files for erdst](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.
@@ -219,5 +219,5 @@
 When the GROMACS runs are done in the example procedures described above,  "../solvent_run.xtc",  "../solvent_run.log", and "../etoh.gro" are the arguments.
 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.

QuickStartGuide-GROMACS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 25 Jul 2025 04:35:59 -0000

--- v64
+++ v65
@@ -100,10 +100,10 @@

 In the following example, the trajectory files for solution system, pure solvent system, isolated solute system are named `solution_run.xtc`, `solvent_run.xtc`, and `solute_run_pbc.xtc`, respectively. The log files are named similarly.

-Generate input configuration for running erdst
+Generate input configuration for solvation free energy calculation
 ----

-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:

 ~~~~sh

QuickStartGuide-GROMACS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 25 Jul 2025 04:32:28 -0000

--- v63
+++ v64
@@ -100,7 +100,7 @@

 In the following example, the trajectory files for solution system, pure solvent system, isolated solute system are named `solution_run.xtc`, `solvent_run.xtc`, and `solute_run_pbc.xtc`, respectively. The log files are named similarly.

-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.

QuickStartGuide-GROMACS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 22 Apr 2025 06:35:50 -0000

--- v62
+++ v63
@@ -176,7 +176,7 @@

 ~~~~sh
 cd ../refs
-(ERmod directory)/share/ermod/tools/GROMACS/gen_input --traj ../solvent_run.xtc --log ../solvent_run.log --flexible ../solute_run_pbc.xtc
+(ERmod directory)/share/ermod/tools/GROMACS/gen_input --traj ../solvent_run.xtc --log ../solvent_run.log --flexible ../solute_run.xtc
 (ERmod directory)/bin/erdst
 ~~~~

QuickStartGuide-GROMACS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 22 Apr 2025 06:32:05 -0000

--- v61
+++ v62
@@ -107,7 +107,7 @@
 First, execute the following command to generate system information:

 ~~~~sh
-(ERmod directory)/share/ermod/tools/gromacs/gen_structure --top etohsolution.top
+(ERmod directory)/share/ermod/tools/GROMACS/gen_structure --top etohsolution.top
 ~~~~

 where (ERmod directory) is the directory where the ERmod programs are installed; the directory was specified with the option of --prefix of ./configure described in [General build guide](build-Guide).
@@ -148,7 +148,7 @@

 ~~~~sh
 cd soln
-(ERmod directory)/share/ermod/tools/gromacs/gen_input --traj ../solution_run.xtc --log ../solution_run.log
+(ERmod directory)/share/ermod/tools/GROMACS/gen_input --traj ../solution_run.xtc --log ../solution_run.log
 ~~~~

 The trajectory (xtc file) and log files are fed to the script
@@ -176,7 +176,7 @@

 ~~~~sh
 cd ../refs
-(ERmod directory)/share/ermod/tools/gromacs/gen_input --traj ../solvent_run.xtc --log ../solvent_run.log --flexible ../solute_run_pbc.xtc
+(ERmod directory)/share/ermod/tools/GROMACS/gen_input --traj ../solvent_run.xtc --log ../solvent_run.log --flexible ../solute_run_pbc.xtc
 (ERmod directory)/bin/erdst
 ~~~~

@@ -210,7 +210,7 @@

 ~~~~sh
 cd ../refs
-(ERmod directory)/share/ermod/tools/gromacs/gen_input --traj ../solvent_run.xtc --log ../solvent_run.log --rigid ../etoh.gro
+(ERmod directory)/share/ermod/tools/GROMACS/gen_input --traj ../solvent_run.xtc --log ../solvent_run.log --rigid ../etoh.gro
 (ERmod directory)/bin/erdst
 ~~~~

QuickStartGuide-GROMACS modified by Shun Sakuraba

Shun Sakuraba — Sun, 28 Apr 2024 10:10:56 -0000

--- v60
+++ v61
@@ -49,7 +49,7 @@
 gmx grompp -f nvt.mdp -c solution_min.gro -p etohsolution.top -o solution_nvt.tpr
 gmx mdrun -s solution_nvt.tpr -o solution_nvt.trr -x solution_nvt.xtc -e solution_nvt.edr -g solution_nvt.log -c solution_nvt.gro
 gmx grompp -f npt.mdp -c solution_nvt.gro -p etohsolution.top -o solution_npt.tpr
-gmx mdrun -s solution_npt.tpr -o solution_npt.trr -x solution_npt.xtc -e solution_npt.edr -g solution_npt.log -c solution_npt.gro
+gmx mdrun -s solution_npt.tpr -o solution_npt.trr -x solution_npt.xtc -e solution_npt.edr -g solution_npt.log -c solution_npt.gro -cpo solution_npt.cpt
 # If you are using GROMACS <= 2020, or want to use anisotropic scaling, use "pcouple = Parrinello-Rahman" instead of "C-rescale" in mdp files. 
 # Note when you use P-R, it is advised you remove first ca. 100 ps from the trajectory, as there will be an initial box fluctuation.
 # To prevent it please check "-cpo" checkpointing in mdrun and "-t" option in grompp.

QuickStartGuide-GROMACS modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 11 Apr 2024 09:25:21 -0000

--- v59
+++ v60
@@ -96,7 +96,7 @@
 2. Use same box size as solvent system, PME, and exactly same configurations as solution/solvent system, e.g. coulombtype=PME, rcoulomb=1.2, vdwtype=Cut-off, rvdw=1.2 in this case.

 (1) is good because it significantly save your calculation time. The approximation error originates from vdW energy difference (rvdw=1.2 vs. rvdw=2.0). As long as you are using long vdw cutoff in solution/reference system (say >= 1.2 nm), this method is probably superior. In this case vdw energy between 1.2 nm to 2.0 nm is almost negligible and will not likely affect the sampling. This tutorial uses this approximation.
-(2) is time-consuming to simulate but theoretically better. This can also be used with smaller vdw cutoff in solution/solvent system. If you want to use this method, you need to disable self energy reweighting (`wgtslf=0` in `refs/parameters_er`; see [Parameter files for erdst](parameters-erdst)). Also, you will probably want to change the sampling length (50ns) to much shorter one. In this tutorial we are using sampling time of 50 ns just because the simulation is fast enough with method (1) and no reason to run long for this sized molecule.  Its convergence depends on molecule types but it should be fast enough for small molecules. If it's slow-converging you will need methods for reweighting anyway.
+(2) is time-consuming to simulate but theoretically better. This can also be used with smaller vdw cutoff in solution/solvent system. If you want to use this method, you need to disable self energy reweighting (`wgtslf=0` in `refs/parameters_er` and `slfslt='not'` in `parameters_fe`; see [Parameter files for erdst](parameters-erdst) and [Parameter files for slvfe](parameters-slvfe)). Also, you will probably want to change the sampling length (50ns) to much shorter one. In this tutorial we are using sampling time of 50 ns just because the simulation is fast enough with method (1) and no reason to run long for this sized molecule.  Its convergence depends on molecule types but it should be fast enough for small molecules. If it's slow-converging you will need methods for reweighting anyway.

 In the following example, the trajectory files for solution system, pure solvent system, isolated solute system are named `solution_run.xtc`, `solvent_run.xtc`, and `solute_run_pbc.xtc`, respectively. The log files are named similarly.

QuickStartGuide-GROMACS modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 08:49:09 -0000

--- v58
+++ v59
@@ -93,10 +93,10 @@
 We have two good approximations:

 1. Run with cutoff larger than molecule diameter e.g. coulombtype=Cut-off, rcoulomb=2.0, vdwtype=Cut-off, rvdw=2.0. 
-2. Use PME, e.g. coulombtype=PME, rcoulomb=1.2, vdwtype=Cut-off, rvdw=1.2.
+2. Use same box size as solvent system, PME, and exactly same configurations as solution/solvent system, e.g. coulombtype=PME, rcoulomb=1.2, vdwtype=Cut-off, rvdw=1.2 in this case.

 (1) is good because it significantly save your calculation time. The approximation error originates from vdW energy difference (rvdw=1.2 vs. rvdw=2.0). As long as you are using long vdw cutoff in solution/reference system (say >= 1.2 nm), this method is probably superior. In this case vdw energy between 1.2 nm to 2.0 nm is almost negligible and will not likely affect the sampling. This tutorial uses this approximation.
-(2) is time-consuming to simulate but may accept small vdw in solution/solvent system. If you want to use this method, you will probably want to change sampling length (50ns) to much shorter one. Currently we are using sampling time of 50 ns just because the simulation is fast enough with method (1).  Its convergence depend on molecule types but it should be fast enough (if not consider using e.g. replica exchange).
+(2) is time-consuming to simulate but theoretically better. This can also be used with smaller vdw cutoff in solution/solvent system. If you want to use this method, you need to disable self energy reweighting (`wgtslf=0` in `refs/parameters_er`; see [Parameter files for erdst](parameters-erdst)). Also, you will probably want to change the sampling length (50ns) to much shorter one. In this tutorial we are using sampling time of 50 ns just because the simulation is fast enough with method (1) and no reason to run long for this sized molecule.  Its convergence depends on molecule types but it should be fast enough for small molecules. If it's slow-converging you will need methods for reweighting anyway.

 In the following example, the trajectory files for solution system, pure solvent system, isolated solute system are named `solution_run.xtc`, `solvent_run.xtc`, and `solute_run_pbc.xtc`, respectively. The log files are named similarly.

@@ -117,7 +117,7 @@
 In the example case, the ethanol molecule is the solute; type “Ethanol” (do not include quotation marks) to proceed.
 After the execution, two directories are created, namely soln and refs.
 Inside these directories, `soln/MDinfo`, `soln/MolPrm1`, `soln/SltInfo`, `refs/MDinfo`, `refs/MolPrm1`, and `refs/SltInfo` files are generated.
-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.
 If gen_structure terminates with an error message about the molecule type, see the top of this page and try
 ~~~~sh
 source (path to gromacs)/bin/GMXRC

QuickStartGuide-GROMACS modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 07:07:27 -0000

--- v57
+++ v58
@@ -4,12 +4,12 @@
 MD Preparation
 ----

-Prepare the latest Gromacs, and install programs according to GROMACS’s documentation. In the following explanation ERmod package is installed under `/path/to/ermod` and the GROMACS installation directory is assumed to be `/path/to/gromacs`. Also, *GROMACS is assumed to be installed without any suffix* (without `_d` / `_mpi`). If you compiled GROMACS with these suffixes, replace `gmx` with an appropriate program name.
+Prepare the latest Gromacs, and install programs according to GROMACS’s documentation. In the following explanation ERmod package is installed under `(ERmod directory)` and the GROMACS installation directory is assumed to be `/path/to/gromacs`. Also, *GROMACS is assumed to be installed without any suffix* (without `_d` / `_mpi`). If you compiled GROMACS with these suffixes, replace `gmx` with an appropriate program name.

 Set PATH for GROMACS. User should be able to run `gmx` (GROMACS 2016 or later) without errors. Otherwise, set path to GROMACS by:

 ~~~~sh
-source (path to gromacs)/bin/GMXRC
+source /path/to/gromacs/bin/GMXRC
 ~~~~

 And test whether `gmx` runs without problem. If they do not work, see the GROMACS installation manual.

QuickStartGuide-GROMACS modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 07:06:40 -0000

--- v56
+++ v57
@@ -199,7 +199,7 @@
 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 erdst 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-ermod03) 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.