Re: [ESPResSo-users] Error

[Olaf Lenz]

Hi!

On 03/30/2011 11:25 AM, Muhammad Anwar wrote:
> After simulation when i watch trajectories using VMD, particle do
> not move, message on terminal is like this
> 
> Info) Determining bond structure from distance search ... ERROR) 
> MolAtom 407: Exceeded maximum number of bonds (12). ERROR) MolAtom 
> 1145: Exceeded maximum number of bonds (12). ERROR) MolAtom 1152: 
> Exceeded maximum number of bonds (12). ERROR) MolAtom 1155: Exceeded
>  maximum number of bonds (12).

This is an issue of VMD, not ESPResSo. If you trajectory file doesn't
contain bond information, VMD assumes you are looking at atomistic data
with a length unit of 1Å, so it tries to compute them automatically,
based on some heuristics about atom names and distances. As in a
coarse-grained model, the length unit is different and the atom names
are just names, this sometimes causes lots of bonds to be generated.
However, the message shouldn't harm you.

> The number of fragments become 852, i think fragments should be equal
> to
number of chains, am i right?

The fragments in VMD are determined via the bond structure, and as that
one is broken in a coarse-grained model, it won't work.

In what format do you output the trajectory? It looks to me as though
you are using PDB, right? I would recommend to use the VTF format, where
you can keep the whole trajectory in a single file, and it also stores
the bond information. Then it doesn't have this problem.

Olaf


-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607

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