Re: Bonds are too long after simulation

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 07 2011 - 13:18:26 CDT

tony,

[...]

> When I look at the output, the minimization was long enough and the system
> looks quite stable at the end of the simulation. However, I do get some
> abnormalities when I look at the structure into VMD: the bonds get bigger
> during the simulation.

apart from what was already mentioned, there is also
the possibility, that this is an artifact of the visualization.
how do you load the trajectory into VMD. the psf file plus
the dcd file or the pdb file plus the dcd file?

in the latter case, you may be seeing spurious bonds
from the heuristic guess that VMD does when loading
.pdb file in contrast to loading a .psf file, where VMD
uses the bond information encoded in the .psf file.

[...]

> The bonds are bigger but they are not huge. From what I've seen in the
> forum, a lot of people have similar issues except that they got huge bonds

this is usually due to per-atom "coordinate wrapping"
that can have bond reach across periodic boundaries.

[...]

> Is is normal that the bond length increases with the simulation? Is there a
> way to fix this?

no. you should not ask how to correct this,
but you should first find out where this originates from.
there may be a trivial explanation or a serious problem
without parameter set. just using some "magic tricks"
to make it go away, might just generate "greater evil"
down the line.

cheers,
     axel.

> I would really appreciate your help as I have no idea how to fix this.
> Please let me know if you need further details about the simulation.
>
> Best regards,
>
> Tony
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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