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

NAMD GROMACS namd.gromacs at gmail.com
Fri Sep 5 06:22:35 CEST 2008


I have a couple of questions regarding top file and forcefield.

1st, in the top file

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
    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.
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.

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


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