Re:Re: Re: Re:Re: Re: Re: Re: Dielectric Constant

From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Wed May 05 2010 - 09:45:20 CDT

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 for1-4 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,
 
 
 
 
   

2010-05-04 21:03:08"Axel Kohlmeyer" <akohlmey_at_gmail.com> д
>> 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.
>

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