write out the correct gro file after truncation!

graeter-group · Nov 15, 2024 · edaff31 · edaff31
1 parent abe31f7
commit edaff31
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Showing 2 changed files with 16 additions and 12 deletions.
diff --git a/src/kimmdy/runmanager.py b/src/kimmdy/runmanager.py
@@ -618,6 +618,7 @@ def _run_md(
         files.input["mdp"] = md_config.mdp
         mdp = files.input["mdp"]
         ndx = files.input["ndx"]
+        logger.info(f"Using the following input files: top: {top}, gro: {gro}")
 
         # to continue MD after timeout
         if continue_md:

diff --git a/src/kimmdy/utils.py b/src/kimmdy/utils.py
@@ -457,24 +457,14 @@ def truncate_sim_files(
             f"Truncating trajectories to {time:.4} ps. Trajectory time was {last_time:.4} ps"
         )
 
-    # backup the tails of trajectories
-    for trj in trjs:
-        tmp = trj.rename(trj.with_name("tmp_backup_" + trj.name))
-        if keep_tail:
-            run_gmx(
-                f"gmx trjconv -f {tmp} -b {time} -o {trj}",
-            )
-            trj.rename(str(trj) + ".tail")
-
-        run_gmx(f"gmx trjconv -f {tmp} -e {time} -o {trj}")
-        tmp.unlink()
 
     # backup the gro
     bck_gro = paths["gro"].rename(
         paths["gro"].with_name("tmp_backup_" + paths["gro"].name)
     )
+    # write out gro at the specified time
     sp.run(
-        f"gmx trjconv -f {trjs[0]} -s {bck_gro} -dump -1 -o {paths['gro']}",
+        f"gmx trjconv -f {trjs[0]} -s {bck_gro} -dump {time} -o {paths['gro']}",
         text=True,
         input="0",
         shell=True,
@@ -483,6 +473,19 @@ def truncate_sim_files(
     if not keep_tail:
         bck_gro.unlink()
 
+    # backup the tails of trajectories
+    for trj in trjs:
+        tmp = trj.rename(trj.with_name("tmp_backup_" + trj.name))
+        if keep_tail:
+            run_gmx(
+                f"gmx trjconv -f {tmp} -b {time} -o {trj}",
+            )
+            trj.rename(str(trj) + ".tail")
+
+        run_gmx(f"gmx trjconv -f {tmp} -e {time} -o {trj}")
+        tmp.unlink()
+
+
     # backup the edr
     if paths["edr"] is not None:
         bck_edr = paths["edr"].rename(