On Fri, Feb 25, 2005, Ilyas Yildirim wrote:
>
> I have a question about vlimit. I have a system which is a methane
> molecule with 3 dummy atoms connected to one of the hydrogen atom. I am
> using this system to transform the methane to ethane molecule in water.
>
> Then, I set the dt=0.001 and run the same simulation. Now, I dont get any
> vlimit problem, and the trajectory file gives a nice/smooth movie in VMD.
This is not surprising. Using dt=0.002 is at the edge of stability, and
assumed that all hydrogen atoms are SHAKEn. But Amber does not allow atoms
that are being perturbed to be used with SHAKE, so you essentially are asking
for trouble using dt=0.002.
.....dac
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Received on Mon Feb 28 2005 - 17:53:01 PST
