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

[Xavier Periole]

On Thu, 4 Sep 2008 23:22:35 -0500
  "NAMD GROMACS" <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) ...

> 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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