Re: vmd-l: Interactive Simulations, ligand size limits....

From: John Stone (
Date: Wed Apr 20 2005 - 16:12:20 CDT

  How large is the molecule you're simulating? When you say that
the simulation "crashed", does that mean that NAMD aborted because
you pulled too hard (margin violation, exceeding the speed of light,
etc...), or did NAMD actually have a seg fault or floating point exception
of some kind? If you got a "margin violation" it means that you pulled
on the structure so hard that you exceeded NAMD's internal limit on
atom velocity imposed by the spatial decomposition it uses. If you
pull to hard and impart a tremendous velocity per simulated timestep,
this means that either you need to pull more gently, or you need to
decrease the gap in timescale between your real-time pulling and
the rate of simulated time in the simulation, either by using a smaller
molecule or by using fixed atoms, or some combination of both.

  John Stone

On Tue, Apr 19, 2005 at 10:51:52PM -0500, Luis Rosales wrote:
> Hi all,
> I just finished a set of tests on interactive dynamics with NAMD2 and VMD on
> a remote server ...
> Basically, I was trying to refine a dimeric protein (around 80 residues each
> monomer), however each time that I tried to move one of the monomers, the
> remote server killed the simulation. (I made sure the system was well
> equilibrated and minimized beforehand, also, i am working in vacuo).
> Wondering if the size of the molecule i was trying to move was too big I
> started to edit one of the monomers, removing residues. At the end I found
> that under my test conditions I am able to move a max of 15 residues without
> problems.
> I would like to know the reason behind this limit, is based on my machines
> (the remote server and the local workstation??), based on limitations of my
> network?? or the VMD/NAMD interface???
> Is possible to modify/overcome this limits?
> Thanks in advance for your advice on this one,
> kind regards,
> Luis
> PS: the remote server is An alpha server SC45, true unix 5.1b, and I was using
> 2 nodes (total 4 processors) with 2 Gb of RAM.

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