From: L. Michel Espinoza-Fonseca (
Date: Tue Aug 22 2006 - 21:18:06 CDT

Hi John,

Thanks for helping me with this. I've done what you suggested and yes,
when I load both psf and pdb files into VMD, they almost used most of
the RAM I have available. I did it only running VMD with no graphical
interface and no other program that can use that memory. It if fine
while I'm not running autoionize. Then the requirement or memory goes
up to 3.6 GB and after a while it crashes.

Maybe we can try the version of VMD that you're going to release,
although I can wait for a couple of days if it coutd get you into some
troubles. Hopefully this time it'll work out.

Thanks a lot!

2006/8/22, John Stone <>:
> Michel,
> I'm having a look at the structure. So far I've observed a few things
> just loading the structure into a fresh VMD session with nothing else
> loaded already:
> When loading PSF followed by PDB:
> - Loading the 8 million atom PSF file uses 1.8GB of memory if nothing else
> has been loaded yet. (mol new huge.psf)
> - Loading in the 8 million tom PDB subsequent to the PSF file brings the
> total memory use up to 2.6GB (mol addfile huge.pdb)
> When loading the PDB followed by PSF (causes the distance-based bond
> search to run unless you tell it not to, and some atoms get excessive
> numbers of bonds and thus VMD complains...):
> - Loading the 8 million atom PDB file uses 2.9GB of memory if nothing else
> has been loaded yet. (mol new huge.pdb)
> - Loading in the 8 million tom PSF subsequent to the PDB file brings the
> total memory use up to 3.5GB (mol addfile huge.psf)
> Just judging from what I've observed here loading your PDB and PSF files,
> it looks to me like you're running the system out of memory, as even with
> 4GB of memory, Linux (or whatever you're running) is using some of that for
> the kernel, the windowing system, and for filesystem buffers. However, all
> is not lost. If you load the PSF file first and the PDB file second you can
> save almost 1GB of memory due to decreased memory fragmentation. Some malloc
> implementations are smarter than others. On the 32GB Sun machine I tested
> on, it didn't coalesce the tiny bits of memory very well, so (on that system
> at least) there's a big advantage to loading the PSF first and the PDB
> second not only because you can skip the autobonds search, but also due to the
> reduced memory fragmentation etc.
> When you ran autoionize, I'm guessing what happened is that you were loading
> in these huge structures in addition to the starting structures you already
> had loaded, and from the numbers I gave above, that would clearly lead to
> disaster, as you'd need more like 8GB of RAM in order to have multiple
> 8 million atom structures loaded at once. One way to prevent this would
> be to use the structure building tools via their text command interfaces,
> which should allow you to create the new structures without auto-loading
> them back into VMD when each step is finished. You could then run the
> tools one at a time, deleting the previous molecules before moving on to
> the next step, in order to minimize the memory footprint you've got going
> during each step.
> Now, I have to mention that I ran my test using VMD 1.8.5, which uses
> a little more memory per-atom than VMD 1.8.4 did, as it allows more bonds
> per atom, but my results should be an upper bound on the amount of memory
> needed to load your systmem.
> Try loading the PSF file, followed by the PDB, and let me know if you
> succeed with that. If that still puts you dangerously close to running out
> of memory, I can try giving you a modified version of VMD that uses a bit
> less memory per-atom than the one you're using, though it'll have to wait
> until after I finish releasing VMD 1.8.5. You can also increase the swap
> space on your system and try working when the machine has little or no other
> processes running.
> Worst case, if you are maxed out at 4GB of ram, and you can't get this
> done, I can run the tools for you on our 32GB machine and provide the
> output files to you. I'd like to find a way for you to run this on the
> 4GB machine you have however, and I think that with some attention to details
> and running things more manually, it should be doable.
> John Stone
> On Tue, Aug 22, 2006 at 05:36:39PM -0500, L. Michel Espinoza-Fonseca wrote:
> > Hi John,
> >
> > It's me again. This time I got a problem where I'm unable to get any
> > solution. I'm trying to add ions to a fairly big system (this time
> > something around 8,000,000 atoms). I can solvate it with no problems,
> > but when I try to run autoionize, I get the following:
> >
> > reading topology file
> > /home/bscl2/espinoza/lib/vmd/plugins/noarch/tcl/autoionize1.2/
> > >>>>>> SOD and CLA Ions Topology File <<<<<<<<<
> > extracted from
> > >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> > >>>>>>>>>>>>>>>>>>>>>August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> > >>>>>>>Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> > >>>>>>410-706-7442 or email: alex, <<<<<<<<<
> >
> > Created by CHARMM version 27 1
> >
> > Autoionize) Reading monster-water.psf/monster-water.pdb...
> > clearing structure, preserving topology and aliases
> > reading structure from psf file monster-water.psf
> > reading coordinates from pdb file monster-water.pdb
> > psfplugin) Detected a Charmm31 PSF file
> > Info) Using plugin psf for structure file monster-water.psf
> > Segmentation fault
> >
> > And of course VMD crashes. I made stacksize and coredumpsized
> > unlimited, but I got the same thing (VMD crashes). Do you have any
> > suggestions on how to solve the problem? I'm using a workstation with
> > 2 double-core Opteron and 4 GB of RAM.
> >
> > Thanks!
> >
> > Michel
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: Phone: 217-244-3349
> WWW: Fax: 217-244-6078