[gmx-users] OPLS and RB parameters in GROMACS

[sulatha M. S]

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

                                 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> 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> 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
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110209/9326a4dc/attachment.html>