Gromacs trajectory: not enough memory

[mauricio.martin@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open //wsl.localhost/Ubuntu-22.04/home/emmartin/ArcB/long_sim.gro

Summary of feedback from opening
//wsl.localhost/Ubuntu-22.04/home/emmartin/ArcB/long_sim.gro  
---  
note | Singleton residues assigned chain ID B  
  
Chain information for AEROBIC RESPIRATION CONTROL SENSOR PROTEIN in water #1  
---  
Chain | Description  
A | No description available  
  

> open //wsl.localhost/Ubuntu-22.04/home/emmartin/ArcB/long_sim.xtc

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 118, in open  
num_coords = read_coords(session, data, structure_model, md_type,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 80, in read_coords  
model.add_coordsets(coords, replace=replace)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1771, in add_coordsets  
f(self._c_pointer, replace, pointer(xyzs), *xyzs.shape[:2])  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1771, in add_coordsets  
f(self._c_pointer, replace, pointer(xyzs), *xyzs.shape[:2])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 596.08
OpenGL renderer: NVIDIA GeForce RTX 4050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: es_MX.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Dell G15 5530
OS: Microsoft Windows 11 Home Single Language (Build 26200)
Memory: 16,849,256,448
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i7-13650HX
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
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    ChimeraX-AddCharge: 1.5.19
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[Eric Pettersen]

Hi Eduardo,

Thanks for reporting this problem. Firstly, you should upgrade to the 1.12 release candidate because it has several changes that make trajectory reading more memory efficient. Nonetheless, if you have a really big coordinate file it might run out of memory anyway. In that case, try using the "step" keyword in order to read fewer frames (e.g. "step 5" for every fifth frame).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab