Hi,
I want to pertub a TIP3 water to a dummy water (with 0- charge and 0 vdw
constants, but with TIP3P bond properties) and at the same time pertub a
dummy water to a TIP3P water. In my previous mail I got the response:
"Also, TIP3P water is by definition rigid (enforced in Amber by SHAKE), but
Amber does not currently allow atoms that are being perturbed to undergo
SHAKE. So, your problem may be difficult to implement without modifications
to the code."
And also David wrote as:
> Yes: this is correct. The perturbation code turns of shake for any atoms
> that are being pertubed. SHAKE on non-perturbed atoms would still be there
> if SHAKE is turned on with the ntc variable.
> Unfortunately, this restriction makes it very difficult to perturb water
> molecules, which need to be rigid in most simple models, like TIP3 or TIP4.
> We will try to put together a fix for this limitation.
Without changing the code is it not possible to turn off the shake for water?
If we have to change the code where and what should I do?
Thanks,
Turgut
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Received on Tue Aug 10 2004 - 01:53:00 PDT
