[gmx-users] ff parameters,

rama david ramadavidgroup at gmail.com
Sat Nov 10 14:47:01 CET 2012


Hi justin,
If you dont mind please give the link for gromacs 4 paper , it will surely
help
me to decide ff and parameter...

Thank you in advance,

With best wishes and regards,
Rama david


On Sat, Nov 10, 2012 at 6:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/10/12 7:09 AM, Ali Alizadeh wrote:
>
>> Dear Rama
>>
>> Thank you for your reply dear Rama,
>>
>> I'm really sorry,
>>
>> My link was wrong,
>>
>> This link is correct:
>>
>> cinjweb.umdnj.edu/~kerrigje/**pdf_files/fwspidr_tutor.pdf<http://cinjweb.umdnj.edu/~kerrigje/pdf_files/fwspidr_tutor.pdf>
>>
>> Of course this tutorial do not use opls-aa but it says some of
>> parameters about opls ff .(page-4)
>>
>>
> I have no idea where these parameters come from (even the ones in Berk's
> notes).  I have never seen people use such settings with Gromos96, and
> those listed in the table conflict with the protocols in the Gromos96
> literature.  Settings for OPLS-AA are less clear.  It is very common to use
> 1.0-nm cutoffs (and in fact was the case in the Gromacs 4 paper), though
> the original OPLS literature used different cutoffs depending upon what
> types of molecules were present, which is not possible in Gromacs.  You
> should read lots of papers by people who use OPLS-AA for similar types of
> systems and evaluate their success or inaccuracies.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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