From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Fri Feb 27 2015 - 13:58:31 CST
Hi Mehran,
"I was wondering if there is a way to scale Lj parameter only for
specific pairs". CHARMM-format parameter files contain NBFIX sections
that allow you to set LJ parameters for specific pairs. For instance,
the Luo and Roux corrections to obtain correct osmotic pressure for
NaCl and KCl solutions:
NBFIX
! Emin Rmin
! (kcal/mol) (A)
SOD CLA -0.083875 3.731 ! From osmotic pressure
calibration, J. Phys.Chem.Lett. 1:183-189
POT CLA -0.114236 4.081 ! From osmotic pressure
calibration, J. Phys.Chem.Lett. 1:183-189
Note that for NBFIX you give Rmin and not Rmin/2 as in the NONBONDED
section of CHARMM parameter files.
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Fri, Feb 27, 2015 at 1:15 PM, MEHRAN MB <mb.mehran1_at_gmail.com> wrote:
> Dear NAMD user,
>
> I am simulating a protein system in presence of TMAO molecule in which I
> used the most updated charmm general force field for TMAO. Most of
> simulation studied of TMAO have employed Kast model. Garcia et al showed
> that this TMAO model, Kast model, does not provide acceptable osmotic
> pressure compare to experimental results ( Molecular Mechanism for the
> Preferential Exclusion of TMAO from Protein Surfaces, J. Phys. Chem. B,
> 2012, 116 (40), pp 12095–12104). They improved this model by decreasing Lj
> potential well only for TMAO-TMAO interactions which make them less
> favorable to each other and TMAO-water remained the same. To applying their
> model into my system and compare it with charmm results, I was wondering if
> there is a way to scale Lj parameter only for specific pairs, for instance
> all TMAO-TMAO, in NAMD?!
>
>
> Best,
> Mehran
> UOttawa
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