[gmx-users] OPLS and RB parameters in GROMACS

[Mark Abraham]

On 9/02/2011 4:48 PM, sulatha M. S wrote:
> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 
> 121, 20, 4831, 1999), the aliphatic torsional parameters are the same 
> as those from 1996. here are the values,
>
>
>                                    V1                    
> V2                    V3 (kcal/mol)
> CT-CT-CT-CT              1.740               -0.157                 0.279
>
> HC-CT-CT-CT              0.000                0.000                0.366
>
> HC-CT-CT-HC             0.000                 0.000               0.318
>
>
> Values calculated from the equation given in p.62 of the manual in 
> kJ/mol are

I can see nothing relevant on p62 of the 4.5 manual. When giving 
references to literature that exists in multiple versions, please be 
very precise. Giving details such as the manual version number, page 
number, equation number and description of the relationship described in 
the equation will make it much more likely that someone will (want to) 
(be able to) help you.

Mark

>
>                                  c0                       c1 
>                   c2                         c3
> CT-CT-CT-CT             3.56686            -1.88907            
> 0.65688                -2.33467
>
> HC-CT-CT-CT              0.66526           1.99577            
> 0.000                     -2.66102
>
> HC-CT-CT-HC             0.76567            -2.29702           
> 0.000                     -3.06269
>
> and the values given in ffoplsaabon.itp are:
>
> CT-CT-CT-CT             2.9288            -1.4644                
> 0.2092               -1.6736
>
> HC-CT-CT-CT             0.6276           1.88280               
> 0.000                  -2.5104
>
> HC-CT-CT-HC             0.6276            1.8828               
> 0.000                   -2.5104
>
> So there is a difference. Which of these is correct ? Any help is 
> highly appreciated.
>
> Sulatha
>
>
>
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch <apaluch at nd.edu 
> <mailto:apaluch at nd.edu>> wrote:
>
>     There is no error. The alkane dihedral parameters were updated in
>     1999, and differ from those originally published in 1996.
>
>     Andrew
>
>     On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S <mssulatha at gmail.com
>     <mailto:mssulatha at gmail.com>> wrote:
>
>         Hi all,
>
>         Hi
>
>           
>
>         I've converted the OPLS-AA torsional potential parameters for the
>
>         alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
>
>         C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
>
>         OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
>
>         to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
>
>         that the calculated values are different.
>
>           
>
>         A previous post to the gmx-users mailing list on March 27, 2008,
>
>         pointed out this issue for the H-C-C-H torsional potential but there was no response to that.
>
>           
>
>         Does anyone know if there is an error in the ffoplsaabon.itp file? Or
>
>         is there a newer set of OPLS-AA parameters?
>
>           
>
>         For the OPLS-AA parameters (in kcal/mol), I used:
>
>           
>
>         dihedral               V1           V2              V3
>
>         C-C-C-C             1.740       -0.157          0.279
>
>         C-C-C-H              0.0           0.0             0.366
>
>         H-C-C-H              0.0           0.0             0.318
>
>           
>
>         from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>
>           
>
>         dihedral               C0            C1              C2            C3
>
>         C-C-C-C             3.56686    -1.889076    0.65688   -2.33467
>
>         C-C-C-H              0.66526    1.99577      0.0            -2.661024
>
>         H-C-C-H              0.76567    -2.29702     0.0            -3.06269
>
>           
>
>         the parameters in the ffoplsaabon.itp file are:
>
>           
>
>         dihedral               C0           C1              C2            C3
>
>         C-C-C-C            2.9288       -1.4644       0.2092      -1.6736
>
>         C-C-C-H            0.6276        1.88280     0.0            -2.5104
>
>         H-C-C-H            0.6276        1.8828       0.0            -2.5104
>
>
>
>         Thankyou for any clarification.
>
>         Sulatha
>
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