On Mon, Oct 03, 2011, Aparna P wrote:
>
> I mean is thre any problem if we fix the bond lenghts as 1.48 instead of
> 1.49?
> When I done simulations with this structure,it showed some problems such as
> velocity limit exceeded etc.
> Is that because of this bond length problem?
It is unlikely that a 0.01 Ang. change in the ideal bond length would
lead to the problems you are seeing. There could be other problems with
your modified benzene system (i.e. that a combination of bond or angle
parameters is not consistent) that leads to such problems. Many other
problems (such as a bad initial structure) can cause such problems as
well, but looking carefully at force field modifiations you have made is a
good start.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 03 2011 - 05:00:04 PDT
