From 49d63f1b9a5721ff91b4ce8c6b8628c8ba4c222b Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Thu, 11 Dec 2025 14:27:21 +0100 Subject: [PATCH 1/9] apply shake to the hydrogens in the beginning to allow Q to solve suboptimal bond geometries from auto-added hydrogens --- src/QligFEP/INPUTS/eq1.inp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/QligFEP/INPUTS/eq1.inp b/src/QligFEP/INPUTS/eq1.inp index e07f0b4f..6c74aeda 100644 --- a/src/QligFEP/INPUTS/eq1.inp +++ b/src/QligFEP/INPUTS/eq1.inp @@ -6,7 +6,7 @@ bath_coupling 0.2 random_seed SEED_VAR initial_temperature 1 shake_solvent on -shake_hydrogens off +shake_hydrogens on shake_solute off lrf on separate_scaling on From f33ec7fac966283b5b6559a19e102f432d39c099 Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Thu, 11 Dec 2025 14:28:39 +0100 Subject: [PATCH 2/9] do not apply shake to the solvents on equilibration steps 2 and 3 --- src/QligFEP/INPUTS/eq2.inp | 2 +- src/QligFEP/INPUTS/eq3.inp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/QligFEP/INPUTS/eq2.inp b/src/QligFEP/INPUTS/eq2.inp index c131bb22..93e9cb6f 100644 --- a/src/QligFEP/INPUTS/eq2.inp +++ b/src/QligFEP/INPUTS/eq2.inp @@ -5,7 +5,7 @@ temperature 50 bath_coupling STEPSIZE shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on +shake_solvent off lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/eq3.inp b/src/QligFEP/INPUTS/eq3.inp index 754baac0..5ec68863 100644 --- a/src/QligFEP/INPUTS/eq3.inp +++ b/src/QligFEP/INPUTS/eq3.inp @@ -5,7 +5,7 @@ temperature 150 bath_coupling STEPSIZE shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on +shake_solvent off lrf on separate_scaling on From fe6a150e8548922e93c5cd8f5d86dd114c12cae6 Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Thu, 11 Dec 2025 16:41:40 +0100 Subject: [PATCH 3/9] set shake_solute to be always off --- src/QligFEP/INPUTS/eq5.inp | 2 +- src/QligFEP/INPUTS/md_0000_1000.inp | 2 +- src/QligFEP/INPUTS/md_0500_0500.inp | 2 +- src/QligFEP/INPUTS/md_1000_0000.inp | 2 +- src/QligFEP/INPUTS/md_XXXX_XXXX.inp | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/QligFEP/INPUTS/eq5.inp b/src/QligFEP/INPUTS/eq5.inp index d3159fa5..8ef383c5 100644 --- a/src/QligFEP/INPUTS/eq5.inp +++ b/src/QligFEP/INPUTS/eq5.inp @@ -4,7 +4,7 @@ stepsize STEPSIZE temperature T_VAR bath_coupling 10.0 shake_hydrogens STEPTOGGLE -shake_solute STEPTOGGLE +shake_solute off shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_0000_1000.inp b/src/QligFEP/INPUTS/md_0000_1000.inp index 2b27fa11..16f51874 100644 --- a/src/QligFEP/INPUTS/md_0000_1000.inp +++ b/src/QligFEP/INPUTS/md_0000_1000.inp @@ -4,7 +4,7 @@ stepsize STEPSIZE temperature T_VAR bath_coupling 10 shake_hydrogens STEPTOGGLE -shake_solute STEPTOGGLE +shake_solute off shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_0500_0500.inp b/src/QligFEP/INPUTS/md_0500_0500.inp index dd4bd8f0..ac7d8a51 100644 --- a/src/QligFEP/INPUTS/md_0500_0500.inp +++ b/src/QligFEP/INPUTS/md_0500_0500.inp @@ -4,7 +4,7 @@ stepsize STEPSIZE temperature T_VAR bath_coupling 10 shake_hydrogens STEPTOGGLE -shake_solute STEPTOGGLE +shake_solute off shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_1000_0000.inp b/src/QligFEP/INPUTS/md_1000_0000.inp index b6d0c94e..ccdee6c9 100644 --- a/src/QligFEP/INPUTS/md_1000_0000.inp +++ b/src/QligFEP/INPUTS/md_1000_0000.inp @@ -4,7 +4,7 @@ stepsize STEPSIZE temperature T_VAR bath_coupling 10 shake_hydrogens STEPTOGGLE -shake_solute STEPTOGGLE +shake_solute off shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp index 344a1cda..9dc0317a 100644 --- a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp +++ b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp @@ -4,7 +4,7 @@ stepsize STEPSIZE temperature T_VAR bath_coupling 10 shake_hydrogens STEPTOGGLE -shake_solute STEPTOGGLE +shake_solute off shake_solvent on lrf on separate_scaling on From 2b003672578c4e24dcde3fd4c68c3a257e1ab0a9 Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Thu, 11 Dec 2025 21:41:52 +0100 Subject: [PATCH 4/9] fix bug when passing a custom experimental key --- src/QligFEP/analyze_FEP.py | 49 ++++++++++++++++++++++++++++++++------ 1 file changed, 42 insertions(+), 7 deletions(-) diff --git a/src/QligFEP/analyze_FEP.py b/src/QligFEP/analyze_FEP.py index b9c945ad..f7aee372 100644 --- a/src/QligFEP/analyze_FEP.py +++ b/src/QligFEP/analyze_FEP.py @@ -442,8 +442,18 @@ def load_experimental_data(self, exp_key: str): _to = self.data[self.system][fep]["to"] # search ligands in the edges + ddG = None for edge in self.mapping_json["edges"]: if edge["from"] == _from and edge["to"] == _to: + if exp_key not in edge: + logger.error( + f"Experimental key '{exp_key}' not found in edge {_from} -> {_to}. " + f"Available keys in this edge: {', '.join(edge.keys())}. " + f"Please check your mapping JSON file and ensure the experimental key is correct." + ) + raise KeyError( + f"Key '{exp_key}' not found in edge data. Check your mapping JSON file." + ) ddG = edge[exp_key] break @@ -489,15 +499,40 @@ def populate_mapping_dictionary(self, method, output_file: str | Path | None = N with output_file.open("w") as f: json.dump(self.mapping_json, f, indent=4) - @staticmethod - def prepare_df(json_dict, experimental_data: bool = True): - pref = "dg" if "dg_error" in json_dict["edges"][0] else "ddg" + def prepare_df(self, json_dict, experimental_data: bool = True): df = pd.DataFrame(json_dict["edges"]) if experimental_data: + if self.exp_key is None: + logger.error( + "No experimental key has been set. Call load_experimental_data() first " + "or set experimental_data=False." + ) + raise ValueError("exp_key is None - cannot prepare dataframe with experimental data") + + # For custom keys, edges have "{key}", for our suite they have "ddg_value" or "dg_value" + # First try the key directly for custom keys + expected_col = f"{self.exp_key}" + if expected_col not in df.columns: + # Fall back to checking for standard naming (dg_value/ddg_value) + if "dg_value" in df.columns: + expected_col = "dg_value" + elif "ddg_value" in df.columns: + expected_col = "ddg_value" + else: + available_cols = [col for col in df.columns if "delta_" in col or "_value" in col or "dg" in col.lower()] + logger.error( + f"Expected experimental data column 'delta_{self.exp_key}' not found in edges data. " + f"Available columns that might contain experimental data: {', '.join(available_cols) if available_cols else 'none'}. " + f"Please check that your experimental key '{self.exp_key}' matches the data in your mapping JSON file." + ) + raise KeyError( + f"Column 'delta_{self.exp_key}' not found. Check your mapping JSON file has the correct experimental data." + ) + df = ( df.assign( - ddg_value=lambda x: x[pref + "_value"], - residual=lambda x: x[pref + "_value"] - x["Q_ddG_avg"], + ddg_value=lambda x: x[expected_col], + residual=lambda x: x[expected_col] - x["Q_ddG_avg"], residual_abs=lambda x: x["residual"].abs(), ) .sort_values("residual_abs", ascending=False) @@ -646,7 +681,7 @@ def result_to_latex(res, latexify_each=False): # TODO: move this out of this me # set labels, make it square and add legend plt.title( f"{(target_name + ' ' if target_name is not None else '')}" - r"$\Delta\Delta \text{G}_{\text{BAR}}$ ($\mathrm{N}=" + r"$\Delta\Delta \mathrm{G}_{\mathrm{BAR}}$ ($\mathrm{N}=" f"{len(exp_values)}$)" ) plt.xlabel("$\Delta\Delta G_{exp} (kcal/mol)$") # noqa: W605 @@ -887,7 +922,7 @@ def main(args: argparse.Namespace): results_df = fep_reader.prepare_df(results_json) if fep_reader.ignored_edges: results_df = results_df.query("~fep_name.isin(@fep_reader.ignored_edges)").reset_index(drop=True) - fig, ax = fep_reader.create_ddG_plot(results_df=results_df) + fig, _ = fep_reader.create_ddG_plot(results_df=results_df) fig.savefig(f"{args.target}_ddG_plot.png", dpi=300, bbox_inches="tight") else: results_json = json.loads((Path.cwd() / results_file).read_text()) From 1fae2c07a9f306d6a598f77741eb0ffce0ec35c6 Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Thu, 11 Dec 2025 21:48:07 +0100 Subject: [PATCH 5/9] improve comments and error messages --- src/QligFEP/analyze_FEP.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/QligFEP/analyze_FEP.py b/src/QligFEP/analyze_FEP.py index f7aee372..33139ed8 100644 --- a/src/QligFEP/analyze_FEP.py +++ b/src/QligFEP/analyze_FEP.py @@ -509,11 +509,10 @@ def prepare_df(self, json_dict, experimental_data: bool = True): ) raise ValueError("exp_key is None - cannot prepare dataframe with experimental data") - # For custom keys, edges have "{key}", for our suite they have "ddg_value" or "dg_value" - # First try the key directly for custom keys + # For custom keys, edges have "delta_{node key}", which needs to be passed by the user + # The keys we use for experimental values are "ddg_value" (edge) or "dg_value" (node) expected_col = f"{self.exp_key}" if expected_col not in df.columns: - # Fall back to checking for standard naming (dg_value/ddg_value) if "dg_value" in df.columns: expected_col = "dg_value" elif "ddg_value" in df.columns: @@ -521,12 +520,12 @@ def prepare_df(self, json_dict, experimental_data: bool = True): else: available_cols = [col for col in df.columns if "delta_" in col or "_value" in col or "dg" in col.lower()] logger.error( - f"Expected experimental data column 'delta_{self.exp_key}' not found in edges data. " + f"Expected experimental data column '{self.exp_key}' not found in edges data. " f"Available columns that might contain experimental data: {', '.join(available_cols) if available_cols else 'none'}. " - f"Please check that your experimental key '{self.exp_key}' matches the data in your mapping JSON file." + f"Please check for the correct key with experimental value on your mapping JSON file." ) raise KeyError( - f"Column 'delta_{self.exp_key}' not found. Check your mapping JSON file has the correct experimental data." + f"Column '{self.exp_key}' not found. Check your mapping JSON file has the correct experimental data." ) df = ( From d8cc9a1fd20b5fe8627262219cdb0f142a3409e9 Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Mon, 5 Jan 2026 15:13:44 +0100 Subject: [PATCH 6/9] Input files now follow the order when setting SHAKE: solvent, hydrogens, solute. Now, setting the FEP run to 2fs will apply shake to all hydrogens in the simulation. Solvent SHAKE is set to off in case solvent contains other solvents like POPC. shake_hydrogens already handles shake settings for HOH molecules. --- src/QligFEP/INPUTS/eq2.inp | 2 +- src/QligFEP/INPUTS/eq3.inp | 2 +- src/QligFEP/INPUTS/eq4.inp | 2 +- src/QligFEP/INPUTS/eq5.inp | 2 +- src/QligFEP/INPUTS/md_0000_1000.inp | 2 +- src/QligFEP/INPUTS/md_0500_0500.inp | 2 +- src/QligFEP/INPUTS/md_1000_0000.inp | 2 +- src/QligFEP/INPUTS/md_XXXX_XXXX.inp | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/QligFEP/INPUTS/eq2.inp b/src/QligFEP/INPUTS/eq2.inp index 93e9cb6f..295ad263 100644 --- a/src/QligFEP/INPUTS/eq2.inp +++ b/src/QligFEP/INPUTS/eq2.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature 50 bath_coupling STEPSIZE +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent off lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/eq3.inp b/src/QligFEP/INPUTS/eq3.inp index 5ec68863..775c233f 100644 --- a/src/QligFEP/INPUTS/eq3.inp +++ b/src/QligFEP/INPUTS/eq3.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature 150 bath_coupling STEPSIZE +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent off lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/eq4.inp b/src/QligFEP/INPUTS/eq4.inp index 3c270c14..3d50022e 100644 --- a/src/QligFEP/INPUTS/eq4.inp +++ b/src/QligFEP/INPUTS/eq4.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature 275 bath_coupling STEPSIZE +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/eq5.inp b/src/QligFEP/INPUTS/eq5.inp index 8ef383c5..290871e3 100644 --- a/src/QligFEP/INPUTS/eq5.inp +++ b/src/QligFEP/INPUTS/eq5.inp @@ -3,9 +3,9 @@ steps NSTEPS1 stepsize STEPSIZE temperature T_VAR bath_coupling 10.0 +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_0000_1000.inp b/src/QligFEP/INPUTS/md_0000_1000.inp index 16f51874..602b7863 100644 --- a/src/QligFEP/INPUTS/md_0000_1000.inp +++ b/src/QligFEP/INPUTS/md_0000_1000.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_0500_0500.inp b/src/QligFEP/INPUTS/md_0500_0500.inp index ac7d8a51..a9e16c20 100644 --- a/src/QligFEP/INPUTS/md_0500_0500.inp +++ b/src/QligFEP/INPUTS/md_0500_0500.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_1000_0000.inp b/src/QligFEP/INPUTS/md_1000_0000.inp index ccdee6c9..d3a59871 100644 --- a/src/QligFEP/INPUTS/md_1000_0000.inp +++ b/src/QligFEP/INPUTS/md_1000_0000.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on lrf on separate_scaling on diff --git a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp index 9dc0317a..1b1f9ff5 100644 --- a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp +++ b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp @@ -3,9 +3,9 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 +shake_solvent off shake_hydrogens STEPTOGGLE shake_solute off -shake_solvent on lrf on separate_scaling on From eb9a61491799c2e886e184d4d690b7de90f4f94f Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Mon, 5 Jan 2026 16:24:05 +0100 Subject: [PATCH 7/9] use pd.isna(); robust to None and np.NaN; revert prepare_df to staticmethod --- src/QligFEP/analyze_FEP.py | 42 +++++++++++++++++--------------------- 1 file changed, 19 insertions(+), 23 deletions(-) diff --git a/src/QligFEP/analyze_FEP.py b/src/QligFEP/analyze_FEP.py index 33139ed8..a0c0cc7e 100644 --- a/src/QligFEP/analyze_FEP.py +++ b/src/QligFEP/analyze_FEP.py @@ -482,9 +482,9 @@ def populate_mapping_dictionary(self, method, output_file: str | Path | None = N for fep in self.feps: fep_dict = self.data["result"][method][fep] if fep_dict["from"] == _from and fep_dict["to"] == _to: - avg_val = fep_dict[f"{method}_avg"] if not np.isnan(fep_dict[f"{method}_avg"]) else None - sem_val = fep_dict[f"{method}_sem"] if not np.isnan(fep_dict[f"{method}_sem"]) else None - std_val = fep_dict[f"{method}_std"] if not np.isnan(fep_dict[f"{method}_std"]) else None + avg_val = fep_dict[f"{method}_avg"] if not pd.isna(fep_dict[f"{method}_avg"]) else None + sem_val = fep_dict[f"{method}_sem"] if not pd.isna(fep_dict[f"{method}_sem"]) else None + std_val = fep_dict[f"{method}_std"] if not pd.isna(fep_dict[f"{method}_std"]) else None edge.update( { @@ -499,34 +499,30 @@ def populate_mapping_dictionary(self, method, output_file: str | Path | None = N with output_file.open("w") as f: json.dump(self.mapping_json, f, indent=4) - def prepare_df(self, json_dict, experimental_data: bool = True): + @staticmethod + def prepare_df(json_dict, experimental_data: bool = True, exp_key: Optional[str] = None) -> pd.DataFrame: df = pd.DataFrame(json_dict["edges"]) if experimental_data: - if self.exp_key is None: - logger.error( - "No experimental key has been set. Call load_experimental_data() first " - "or set experimental_data=False." - ) - raise ValueError("exp_key is None - cannot prepare dataframe with experimental data") - # For custom keys, edges have "delta_{node key}", which needs to be passed by the user # The keys we use for experimental values are "ddg_value" (edge) or "dg_value" (node) - expected_col = f"{self.exp_key}" - if expected_col not in df.columns: + if exp_key is None: if "dg_value" in df.columns: expected_col = "dg_value" elif "ddg_value" in df.columns: expected_col = "ddg_value" - else: - available_cols = [col for col in df.columns if "delta_" in col or "_value" in col or "dg" in col.lower()] - logger.error( - f"Expected experimental data column '{self.exp_key}' not found in edges data. " - f"Available columns that might contain experimental data: {', '.join(available_cols) if available_cols else 'none'}. " - f"Please check for the correct key with experimental value on your mapping JSON file." - ) - raise KeyError( - f"Column '{self.exp_key}' not found. Check your mapping JSON file has the correct experimental data." - ) + else: + expected_col = exp_key + + if expected_col not in df.columns: + available_cols = [col for col in df.columns if "delta_" in col or "_value" in col or "dg" in col.lower()] + logger.error( + f"Expected experimental data column '{exp_key}' not found in edges data. " + f"Available columns that might contain experimental data: {', '.join(available_cols) if available_cols else 'none'}. " + f"Please check for the correct key with experimental value on your mapping JSON file." + ) + raise KeyError( + f"Column '{exp_key}' not found. Check your mapping JSON file has the correct experimental data." + ) df = ( df.assign( From 631434004917bf141b179b924f9279e9befd858c Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Wed, 7 Jan 2026 12:32:04 +0100 Subject: [PATCH 8/9] shake solvent always set to on since we use rigid water model --- src/QligFEP/INPUTS/eq2.inp | 2 +- src/QligFEP/INPUTS/eq3.inp | 2 +- src/QligFEP/INPUTS/eq4.inp | 2 +- src/QligFEP/INPUTS/eq5.inp | 2 +- src/QligFEP/INPUTS/md_0000_1000.inp | 2 +- src/QligFEP/INPUTS/md_0500_0500.inp | 2 +- src/QligFEP/INPUTS/md_1000_0000.inp | 2 +- src/QligFEP/INPUTS/md_XXXX_XXXX.inp | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/QligFEP/INPUTS/eq2.inp b/src/QligFEP/INPUTS/eq2.inp index 295ad263..b143d636 100644 --- a/src/QligFEP/INPUTS/eq2.inp +++ b/src/QligFEP/INPUTS/eq2.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature 50 bath_coupling STEPSIZE -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/eq3.inp b/src/QligFEP/INPUTS/eq3.inp index 775c233f..22885a5a 100644 --- a/src/QligFEP/INPUTS/eq3.inp +++ b/src/QligFEP/INPUTS/eq3.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature 150 bath_coupling STEPSIZE -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/eq4.inp b/src/QligFEP/INPUTS/eq4.inp index 3d50022e..826e5b19 100644 --- a/src/QligFEP/INPUTS/eq4.inp +++ b/src/QligFEP/INPUTS/eq4.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature 275 bath_coupling STEPSIZE -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/eq5.inp b/src/QligFEP/INPUTS/eq5.inp index 290871e3..fc323715 100644 --- a/src/QligFEP/INPUTS/eq5.inp +++ b/src/QligFEP/INPUTS/eq5.inp @@ -3,7 +3,7 @@ steps NSTEPS1 stepsize STEPSIZE temperature T_VAR bath_coupling 10.0 -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/md_0000_1000.inp b/src/QligFEP/INPUTS/md_0000_1000.inp index 602b7863..de126da6 100644 --- a/src/QligFEP/INPUTS/md_0000_1000.inp +++ b/src/QligFEP/INPUTS/md_0000_1000.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/md_0500_0500.inp b/src/QligFEP/INPUTS/md_0500_0500.inp index a9e16c20..71bce106 100644 --- a/src/QligFEP/INPUTS/md_0500_0500.inp +++ b/src/QligFEP/INPUTS/md_0500_0500.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/md_1000_0000.inp b/src/QligFEP/INPUTS/md_1000_0000.inp index d3a59871..dd6f28a0 100644 --- a/src/QligFEP/INPUTS/md_1000_0000.inp +++ b/src/QligFEP/INPUTS/md_1000_0000.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on diff --git a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp index 1b1f9ff5..46be033b 100644 --- a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp +++ b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp @@ -3,7 +3,7 @@ steps NSTEPS2 stepsize STEPSIZE temperature T_VAR bath_coupling 10 -shake_solvent off +shake_solvent on shake_hydrogens STEPTOGGLE shake_solute off lrf on From 207cf5e49b252ede75c89a29114f2abcd1d0557d Mon Sep 17 00:00:00 2001 From: David-Araripe Date: Wed, 7 Jan 2026 13:31:57 +0100 Subject: [PATCH 9/9] increase the step interval for logging (output), maching non_bond --- src/QligFEP/INPUTS/eq5.inp | 2 +- src/QligFEP/INPUTS/md_0000_1000.inp | 2 +- src/QligFEP/INPUTS/md_0500_0500.inp | 2 +- src/QligFEP/INPUTS/md_1000_0000.inp | 2 +- src/QligFEP/INPUTS/md_XXXX_XXXX.inp | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/QligFEP/INPUTS/eq5.inp b/src/QligFEP/INPUTS/eq5.inp index fc323715..ec465ea4 100644 --- a/src/QligFEP/INPUTS/eq5.inp +++ b/src/QligFEP/INPUTS/eq5.inp @@ -26,7 +26,7 @@ polarisation on polarisation_force 20.0 [intervals] -output 5 +output 25 trajectory 100 non_bond 25 diff --git a/src/QligFEP/INPUTS/md_0000_1000.inp b/src/QligFEP/INPUTS/md_0000_1000.inp index de126da6..21c22cc4 100644 --- a/src/QligFEP/INPUTS/md_0000_1000.inp +++ b/src/QligFEP/INPUTS/md_0000_1000.inp @@ -26,7 +26,7 @@ polarisation on polarisation_force 20.0 [intervals] -output 5 +output 25 energy 10 trajectory 100 non_bond 25 diff --git a/src/QligFEP/INPUTS/md_0500_0500.inp b/src/QligFEP/INPUTS/md_0500_0500.inp index 71bce106..2d47ffb5 100644 --- a/src/QligFEP/INPUTS/md_0500_0500.inp +++ b/src/QligFEP/INPUTS/md_0500_0500.inp @@ -26,7 +26,7 @@ polarisation on polarisation_force 20.0 [intervals] -output 5 +output 25 energy 10 trajectory 100 non_bond 25 diff --git a/src/QligFEP/INPUTS/md_1000_0000.inp b/src/QligFEP/INPUTS/md_1000_0000.inp index dd6f28a0..b05aebfb 100644 --- a/src/QligFEP/INPUTS/md_1000_0000.inp +++ b/src/QligFEP/INPUTS/md_1000_0000.inp @@ -26,7 +26,7 @@ polarisation on polarisation_force 20.0 [intervals] -output 5 +output 25 energy 10 trajectory 100 non_bond 25 diff --git a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp index 46be033b..a0afa84a 100644 --- a/src/QligFEP/INPUTS/md_XXXX_XXXX.inp +++ b/src/QligFEP/INPUTS/md_XXXX_XXXX.inp @@ -26,7 +26,7 @@ polarisation on polarisation_force 20.0 [intervals] -output 5 +output 25 energy 10 trajectory 100 non_bond 25