[gmx-users] buckingham potentials

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> Do u mean to say that all the force fields available in gromacs are 
> default to be used only for LJ potential.
> 

Yes.  That's why they all have their [defaults] directives set to use LJ.

-Justin

> On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     sreelakshmi ramesh wrote:
> 
>         Dear justin,
>                         I am sorry the file is ffG43a1nb.itp.It
>         <http://ffG43a1nb.itp.It> <http://ffG43a1nb.itp.It> was a typing
>         mistake.
> 
> 
>     The points I raised before still stand:
> 
>     1. You're not using 43A1, you're using ffgmx, according to that
>     message from grompp.
> 
>     2. You can't make a simple change to any of the force fields
>     included in Gromacs to magically convert them into using Buckingham
>     potentials.  None of them were designed to do that.  You'll have to
>     basically re-write the entirety of the ff*nb.itp file, and then
>     validate that such a force field model is even valid, because none
>     of them were parameterized to be.
> 
>     -Justin
> 
>         On Wed, Dec 22, 2010 at 9:26 AM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Justin A. Lemkul wrote:
> 
> 
> 
>                sreelakshmi ramesh wrote:
> 
>                    I am using gromos force field fotr my work and This force
>                    field's files come filled
>                     with LJ  functions and now if i want to work with
>                    buckingham potential i changed in default section of
>         force
>                    field ffG34a21.itp file but it gives me the follwing
>         errors
> 
> 
>                    ERROR 77 [file ffgmxnb.itp, line 144]:
>                     Trying to add LJ (SR) while the default nonbond type is
>                    Buck.ham (SR)
> 
> 
>            I should also add that if you think you're using Gromos96
>         (although
>            from "ffG34a21.itp" it's not at all clear to me that you're using
>            any legitimate form of it - 43A1? 43A2? something else?), you're
>            not.  The "ffgmx" force field is a modified form of Gromos87
>         that is
>            antiquated and should not be used for new simulations, as
>         described
>            in detail in the manual.
> 
>            -Justin
> 
> 
>            --     ========================================
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================