[gmx-users] ff parameters,
ramadavidgroup at gmail.com
Sat Nov 10 14:47:01 CET 2012
If you dont mind please give the link for gromacs 4 paper , it will surely
me to decide ff and parameter...
Thank you in advance,
With best wishes and regards,
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:
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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