Interactive Simulations, ligand size limits....

From: Luis Rosales (
Date: Tue Apr 19 2005 - 22:51:52 CDT

 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

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,


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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