From: Hartling, Kathryn (kathryn.hartling_at_cnl.ca)
Date: Wed May 18 2016 - 14:32:24 CDT
UNRESTRICTED / ILLIMITÉE
Dear NAMD users,
Does anyone have advice for simulating TIP4P water in NAMD with flexible bonds?
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 http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/1796.html (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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