From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed May 05 2010 - 21:16:06 CDT
Hi Yandong,
If special 1-4 parameters aren't given, then just use the same
parameters for 1-4 interactions.
Regards,
Dave
On May 5, 2010, at 9:45 AM, ydhuang2727 wrote:
> Hi,
>
> I got the right electrostatic interaction!
>
> For CHARMM22 Force Field, the configure is as follows:
> exclude scaled1-4
> 1-4scaling 1.0
>
> In the namd tutorial, it says:
> The van der Waals interaction for“1-4” atoms are modified using
> special 1-4 parameters defined in the parameter file, which is
> partial shown below.
>
> 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
> !
> !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
> !
> CE2 0.000000 -0.064000 2.080000 !
> ! for ethene, yin/adm jr., 12/95
> CM 0.000000 -0.110000 2.100000 ! ALLOW HEM
> ! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
> CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000
> 1.900000 ! ALLOW ALI
> ! alkane update, adm jr., 3/2/92
> CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000
> 1.900000 ! ALLOW ALI
> ! alkane update, adm jr., 3/2/92
> My question is that, for 1-4 VDW interaction, i may use the
> modified values marked in red for CP1 and CP2, but what for CE2 and
> CM?
>
>
>
> Thanks for your share!
>
>
> Best wishes,
>
> Yandong,
>
>
>
>
>
>
>
> 在2010-05-04 21:03:08，"Axel Kohlmeyer" <akohlmey_at_gmail.com> 写道：
> >> Here comes another question concerning the configure file.
> >> I always use the former parameters in the past, so i have no
> idea which is
> >> superior.
> >>
> >> Will you please tell me, between the above two groups marked in
> red, which
> >> group of parameter is going to get more accurate electrostatic
> interaction?
> >
> >both!
> >
> >which one is the correct one is determined by the force field
> >that you use. for the charmm force field the 1.0 scaling factor
> >is the correct one. it has scaled down 1-4 parameters on
> >some interactions in the parameter file explicitly. it is well
> >documented in the published literature.
> >
> >cheers,
> > axel.
> >
> >>
> >> Cheers,
> >>
> >> Yandong,
> >>
> >--
> >Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> >http://sites.google.com/site/akohlmey/
> >
> >Institute for Computational Molecular Science
> >Temple University, Philadelphia PA, USA.
> >
>
>
> 网易为中小企业免费提供企业邮箱（自主域名）
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/
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