[gmx-users] OPLS group charges

[Erik Lindahl]

Hi,

No - the OPLS charges are calculated from QM, and not tuned to give 
neutral charge groups. The current setup is a compromise between two 
things:

1. It is nice to have charge groups since it speeds up 
neighborsearching and reduces problems from cut-offs
2. Very large charge groups (the whole aminoacid would normally be 
neutral) can give very bad errors  since the cut-off distance is based 
on the group-group center distance.

Btw, if you use PME you don't need charge groups - it is just a way to 
speed up neighborsearching in that case.

Cheers,

Erik

On Nov 5, 2003, at 9:57 AM, Germana Paterlini wrote:

> In skimming through the OPLS charges, I noticed that some amino acids 
> do not have a "charge = 0"
> in each charge group. Some backbone atoms charges are also grouped 
> differently.
> The effect of these is probably minor, since the total charge is 
> correct. Are these just typos?
>
>
> Thanks,
> Germana Paterlini
>
>
>
> Two examples below
>
> [ ARG ]
>
> [ atoms ]
>
> N opls_238 -0.500 1
>
> H opls_241 0.300 1
>
> CA opls_224B 0.140 1
>
> HA opls_140 0.060 1
>
> CB opls_136 -0.120 2
>
> HB1 opls_140 0.060 2
>
> HB2 opls_140 0.060 2
>
> CG opls_308 -0.050 3
>
> HG1 opls_140 0.060 3
>
> HG2 opls_140 0.060 3
>
> CD opls_307 0.190 4
>
> HD1 opls_140 0.060 4
>
> HD2 opls_140 0.060 4
>
> NE opls_303 -0.700 4
>
> HE opls_304 0.440 4
>
> CZ opls_302 0.640 4
>
> NH1 opls_300 -0.800 4
>
> HH11 opls_301 0.460 4
>
> HH12 opls_301 0.460 4
>
> NH2 opls_300 -0.800 4
>
> HH21 opls_301 0.460 4
>
> HH22 opls_301 0.460 4
>
> C opls_235 0.500 5
>
> [ ASN ]
>
> [ atoms ]
>
> N opls_238 -0.500 0
>
> H opls_241 0.300 0
>
> CA opls_224B 0.140 1
>
> HA opls_140 0.060 1
>
> CB opls_136 -0.120 2
>
> HB1 opls_140 0.060 2
>
> HB2 opls_140 0.060 2
>
> CG opls_235 0.500 3
>
> OD1 opls_236 -0.500 3
>
> ND2 opls_237 -0.760 4
>
> HD21 opls_240 0.380 4
>
> HD22 opls_240 0.380 4
>
> C opls_235 0.500 5
>
> O opls_236 -0.500 5
>
>  
>
>  
>
>  
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