From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Fri May 22 2009 - 05:40:00 CDT
I've had a go at a long range dispersion correction, patch is attached. It's the same idea as your water tail correction but it derives an average dispersion coefficient from the whole system rather than only considering water. Also my final expression comes out less visually arresting than yours :-) Using an average dispersion coefficient reduces to the same thing for pure water and is formally correct for any homogeneous mixtures wher g(r) approaches 1 for r > rswitch. I think it's not quite as clear-cut for non-homogeneous protein-water systems but in my opinion it's still better than not applying any correction to the pressure (Shirts et al., J Phys Chem B. 2007 111:13052 convinced me I should be doing this for binding free energy work).
I haven't tested it extensively but I replicated table 1 of the Shirts et al paper (density of pure TIP3P water with PME is no longer sensitive to cutoff) and showed the corrected single point LJ energy for a 900-TIP3P box is stable beyond ~7A while the uncorrected energy approaches the same value asymptotically out to >20A.
I hope it's of some use and that something along these lines ends up in NAMD in the future?
----- Original Message ----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
To: Floris Buelens <floris_buelens_at_yahoo.com>
Sent: Wednesday, 29 April, 2009 16:26:24
Subject: Re: namd-l: water tail correction
To answer the rest of your question (since I realized I didn't do so
before, sorry), the current implementation should work for any
combination of switching/cutoff schemes and water models, since it reads
the former from your simulation parameters and explicitly pulls the VDW
parameters that it needs from the first water molecule in your structure.
Floris Buelens wrote:
> Hi Peter,
> I notice that NAMD 2.7b1 contains an implementation of water tail corrections for energy and pressure - can you give some more details? Is this comparable to the GROMACS dispersion correction scheme? Is this ready for use? Is it general in scope (i.e. independent of water model and cutoff / switching scheme)?
> thanks a lot,
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