Re: CHARMM parameters for H2S

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Sat Jul 19 2008 - 22:34:21 CDT

Raul Araya wrote:
> Dear NAMD users:
>
> Iam planning to perform som MD simulations that involve the use of
> Hydrogen sulfide.
> I wanto to know some things:
> 1) Can one use some parameter already in the charrm top and par files
> to create the H2S molecule?
> 2) If the answer to 1 is NO...are there some H2S parameters avaliable
> or some one who will like to share them?
> 3) Can any one give me some help about how should I parametrize the
> H2S molecule by myself?
>
Dear Raul,
    We developed optimized parameters for H2S that can be found in:
Kamath, Lubna and Potoff, J. Chem. Phys. 123, 124505 (2005). That paper
also has references to all the other significant H2S force fields.

If you use our parameters in NAMD, I suggest a non-bonded cutoff of at
least 14A, since the force field was developed with analytical tail
corrections for the LJ potential.

The topology entry for H2S looks like this (similar to TIP3P water):
MASS 1 H 1.00800 H ! polar H
MASS 2 S 32.06000 S ! sulfur

RESI H2S 0.00
GROUP
ATOM H1 H 0.19 !
ATOM H2 H 0.19 !
ATOM SH2 S -0.38 !

BOND SH2 H1 SH2 H2
ANGLE H1 SH2 H2
PATCHING FIRS NONE LAST NONE

And the parameter file entries:

BONDS
H S 275.000 1.34

ANGLES
H S H 65.136 92.50 0.00 0.00000
 NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
                !adm jr., 5/08/91, suggested cutoff scheme ! NAMD
ignores options
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
H 0.000000 0.000000 0.000000 ! H2S Hydrogen
S 0.000000 -0.461000 2.087500 ! H2S Sulfur

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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