From: John Michael Alex Grime (
Date: Mon Apr 08 2013 - 17:26:12 CDT

Hi all,

I have a single-frame LAMMPs trajectory file which I'm trying to load into VMD.

It's rather large (nearly three million particles, ~133MB), and VMD seems to be struggling a great deal with it. As best as I can tell, the problem might be in the automatic bond detection, as for the last 20 mins or so VMD has been unresponsive and yet the memory usage of VMD is not increasing according to the operating system. I have plenty of memory free, so it would not seem to be an issue with swapping to virtual memory.

I have tried to load this file both using the GUI, and via the following command in the TkConsole:

mol new <the LAMMPS trajectory file> filebonds off autobonds off

... and both of them effectively freeze VMD until I get bored enough to force the program to close. I attached a profiler to the VMD process (using Apple's Instruments suite of software), and got the following stack trace while running:

Running (Self) Symbol Name
230708.0ms 99.9% virtual thunk to vrpn_BaseClass::~vrpn_BaseClass()
230708.0ms 99.9% virtual thunk to vrpn_BaseClass::~vrpn_BaseClass()
230708.0ms 99.9% MoleculeGraphics::~MoleculeGraphics()
230708.0ms 99.9% UIObject::check_event()
230708.0ms 99.9% VolMapCreateCoulombPotentialMSM::VolMapCreateCoulombPotentialMSM(VMDApp*, AtomSel*, float)
230708.0ms 99.9% TclInvokeStringCommand
1.0ms 0.0% vm_map_lookup_entry

I'm not sure if that means anything to anyone, but I thought I might include it just in case.

Does anyone have any suggestions as to what I should be doing to get this to work? I'd be surprised if this is simply impossible in VMD.