From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed May 18 2016 - 17:03:53 CDT
I believe TIP4P is intended to be used with rigid bonds. With flexible
bonds its properties may not be correct.
For instance, the dielectric constant of TIP3P water with rigid bonds is
around 100, while with flexible bonds it's about 170. I imagine you might
see some similar changes in properties with TIP4P.
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
On Wed, May 18, 2016 at 2:32 PM, Hartling, Kathryn <kathryn.hartling_at_cnl.ca>
> UNRESTRICTED / ILLIMITÉE
> Dear NAMD users,
> Does anyone have advice for simulating TIP4P water in NAMD with flexible
> I have successfully implemented a simulation of a TIP4P water box with
> rigid bonds. However, I would like to be able to relax the bonds in order
> to implement a flexible variant of the model. This worked fine with TIP3P,
> but causes the TIP4P models to become unstable and crash. The problem I am
> encountering is similar to that described in thread
> (although I am not using AMBER); the temperature increases rapidly and
> crashes the system despite the use of Langevin dynamics for temperature
> control. The end of the thread states that flexible TIP4P-Ew has
> successfully been run in NAMD before (which is encouraging), but does not
> provide a clear conclusion on what may have caused the problem.
> Some other answers in the archive seem to imply that maybe NAMD TIP4P
> shouldn’t be used with flexible bonds. Can anyone clarify whether TIP4P
> can safely be used with flexible bonds in NAMD? Has anyone encountered
> similar problems and/or does anyone have advice on how best to implement
> flexible TIP4P water in NAMD?
> Thanks very much,
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