Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Mar 19 2008 - 10:38:21 CDT

Well, depends on what you mean by "accuracy". If you have
langevinHydrogen on with rigidbonds you will have calculated
*something*, but many physical properties will be different. I tried
this experiment once with water; I believe I got a diffusion constant
that was about 4x smaller using the same gamma if langevinHydrogen and
rigidbonds were both on, and some other values came out different as
well, so I wouldn't recommend mixing these trajectories with those that
have been run properly.
Hope this helps...
Best,
Peter

Kamilla Kopec wrote:
> *I mean Langevin "hydrogen off" not "hydrogen bonds off".
>
> */Kamilla Kopec <ozero22_at_yahoo.co.uk>/* wrote:
>
> Hi,
>
> I didn't pick up on the fact that "hydrogen bonds off" should be
> used with "rigid bonds all" during my set up and I have a couple
> of trajectories generated with the setting rigid bonds all and
> hydrogen bonds on. Could someone clarify the implications of this
> for the accuracy of the trajectories I have.
>
> Best Regards
>
> Kamilla
>
>
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