From: Ashar Malik (
Date: Fri Jun 02 2017 - 18:59:03 CDT

Hi there,

I think this might have to do with the 4GB memory cap. You can see memory
usage seeing the task managers memory usage graphics while your trajectory

If you collect frames 100 steps apart for a 600ps Simulation -- I am guess
your time step was smaller than 2fs Assuming that it's 1fs you would have
6000 frames.

Two ways would be to make two trajectories with 3000 frame each (or any
number below 5000 frames per trajectory) see "catdcd" for this -- where as
the other other way would be to load smaller parts of the trajectory. To do
this 1 load PSF
2 load trajectory on top of the PSF when you select a dcd or a trajectory
file three boxes underneath the load molecule window will become active.

To load only certain frames use first 0 last -1 and skip 100

This will use the entire trajectory but will load evert 100th frame. You
can change these values in anyway as long as they make sense and load
lesser than 5000 frames (given that your system crashes above 5000)

A third way could be to use catdcd to delete the waters in your Simulation
leaving behind only the protein. This will also reduce the memory needed to
load the trajectory.

Assuming that this is a memory based issue the above suggestions should fix
the problem.


On Jun 3, 2017 09:59, "Fernando Bonilla Millan" <> wrote:

Hello, I'm having an issue trying to load a .psf and its .dcd with 1.9.2
windows version of VMD.
I ran a long MD (600 ps) with a dcdfreq of 100. I ended up with a 1,7 Gb
.dcd file and when I open it with the .psf with VMD it starts loading up
until around 5300 steps until it crashes. It doesnt show any kind of error
on the console, so I assume it's most likely a compatibility issue.
I have ran other long MD but with smaller .dcd, if anyone has any tip, help
or solution to address this problem I would appreciate it, thanks in advance

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