From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Fri Feb 27 2015 - 14:01:29 CST
that is exactly what I am looking for,
I really appreciate your help,
Best,
Mehran
On Fri, Feb 27, 2015 at 2:58 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> 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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