[gmx-users] questions regarding forcefields and .top file

[Justin A. Lemkul]

NAMD GROMACS wrote:
> Hi,
>  
> Can someone please provide me the link? I couldnt find the link in 
> gromacs webpage related to these.also in wiki, this is not clearly 
> described.

A thorough read of Chapter 5 of the manual is probably in order, paying specific 
attention to section 5.3.2 and Table 5.4.

-Justin

> 
> On Fri, Sep 5, 2008 at 2:47 AM, Xavier Periole <X.Periole at rug.nl 
> <mailto:X.Periole at rug.nl>> wrote:
> 
>     On Thu, 4 Sep 2008 23:22:35 -0500
>      "NAMD GROMACS" <namd.gromacs at gmail.com
>     <mailto:namd.gromacs at gmail.com>> wrote:
> 
>         Hi,
> 
>         I have a couple of questions regarding top file and forcefield.
> 
>         1st, in the top file
> 
>         [ angles ]
>         ;  ai    aj    ak funct            c0            c1            c2
>         c3
>           2     1     3     2    ga_9
>           2     1     4     2    ga_9
>           2     1     5     2    ga_10
>           3     1     4     2    ga_9
>           3     1     5     2    ga_10
>         Can you please tell me what the word "funct: stands for? what
>         kind of
>         functionals, why the numbers 2, and then in case of angles it
>         changes to 1?
>         I couldnt find good explanation for this in any manual or tutorial.
> 
>     there is chapter dedicted to this ... and there the wiki (link at
>     www.gromacs.org <http://www.gromacs.org/>) ...
> 
> 
>         Also what does ga_9, ga_10 etc means..I guess the a in ga stands
>         for angle,
>         I dont know where the g is coming from. I am guessing the
>         numbers are
>         different types of bond.
> 
>     you should have a look at the paper of the force field.
> 
> 
>         Question regarding the force-field.
> 
>         Select the Force Field:
>         0: GROMOS96 43a1 force field
>         1: GROMOS96 43b1 vacuum force field
>         2: GROMOS96 43a2 force field (improved alkane dihedrals)
>         3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>         4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>         5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>         6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>         7: [DEPRECATED] Gromacs force field (see manual)
>         8: [DEPRECATED] Gromacs force field with hydrogens for NMR
>         9: Encad all-atom force field, using scaled-down vacuum charges
>         10: Encad all-atom force field, using full solvent charges
> 
>         Here I am choosing 2 for my peptide in water run. I am wondering
>         If I need
>         to study peptide-mineral surface interaction, what number should
>         I chose? Is
>         there a way I can go beyond 10, or can I dvelop my own force
>         field, .top
>         file for interacting with mineral surface? Any suggestions on
>         how to develop
>         new .top file including metals and metal oxide surfaces would be
>         also great
>         help.
> 
>         Thanks
> 
>         Subhashis
> 
> 
>     -----------------------------------------------------
>     XAvier Periole - PhD
> 
>     Molecular Dynamics Group / NMR and Computation
>     University of Groningen
>     The Netherlands
>     -----------------------------------------------------
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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