From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Feb 15 2012 - 15:50:33 CST
Liqun,
The vdwForceSwitching option applies a force-based switching function
to the VDW term. If you don't use the vdwForceSwitching function when
simulating lipids from the CHARMM36 force field, a discrepancy results
between potential energies reported by NAMD and CHARMM (used to
parameterize these lipid force field terms), which yields membrane
surface tensions in NAMD simulations that are between 4-6 dyn/cm
greater than appropriate. Using the vdwForceSwitching function fixes
this problem.
Best,
Chris
On Sat, Feb 11, 2012 at 5:09 PM, Liqun Zhang <lxz79_at_case.edu> wrote:
> Dear namd users:
>
> I read the namd manual online. I found that the explanantion for
> vdwForceSwitching and switching was not clear. I copied the explanation as
> below:
>
> If switching is turned on, then smoothing functions are applied to both the
> electrostatics and van der Waals forces;
>
> If both switching and vdwForceSwitching are set to on, then CHARMM force
> switching is used for van der Waals forces. LJcorrection as implemented is
> inconsistent with vdwForceSwitching.
>
>
> Based on the figure shown, after turning on switching, the energy and
> distance figure should be continuous (energy reaches 0 at cutoff distance).
> After turning on both switching and vdwForceSwitching, the energy and
> distance figure should still be continuous. But what is the difference?
> What is the meaning for CHARMM force switching? Thanks a lot.
>
> Best,
>
> LQZ
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:13 CST