Hi Steven,
2013/3/4 <[email protected]>:
> Dear Votca Users,
>
> I am new to the software. I tried some tutorials but many things are still
> not clear for me as my system is slightly more complex.
Welcome.
>
> My atomistic simulation is one trimer of 3 amino acids in TIP3P water model.
> What I want to extract is just the bonded parameters by IBI between 3 beads
> ech represented by amino acid.
>
> So the key is the tabulated potential of two bonded interactions and one
> angle. My questions:
>
> Does my reference simulation (atomistic) obtained by Gromacs should have [
> exlusions ] of non-bonded parameters so the potentials will be given only
> for bonded? Shall I include in my mdp file while performing atomistic:
> energy_grps so I can use g_energy then to see the bonded potential? I know
> VOTCA does this but not sure based on what kind of trajectory (with excluded
> nonbonded?).
Basically there are two strategies to obtain coarse-grained potential
for bonded interactions.
1.) Separation of bonded and non-bonded. (see Tschoep et al. Acta
Polymerica 49, 61 (1998).)
- run the molecule in vacuum (without solvent) and exclude all
interaction, which are later covered by non-bonded interactions.
- use simple Boltzmann inversion to obtain the bonded interaction (use
csg_stat/awk or csg_boltzmann for that)
- obtain the other interaction by IBI of a cg simulation with the
above bonded interactions fixed (use csg_inverse)
2.) Do IBI on all interaction (use csg_inverse)
- due to our lazyness in the implementation, you will also need
initial guesses for the bonded table here as well and hence you have
to the 2nd step of 1.).
If 1.) or 2.) is better depends a bit on how stiff your bonded
interactions are and hence how good the separation works
Concerning the exclusions, all VOTCA programs tolerate the exclusion
given in the tpr file if you don't map.
If you map first, VOTCA generates its own exclusion, which basically
mean every pair which is connected by a bonded interaction (specified
in the mapping file) is excluded. In both cases, exclusions can be
check using csg_dump --excl (together with --cg for mapped
trajectories).
>
> Presuming I got my 3 bonded potentials (table.xvg). Shall i use in my CG
> run:
>
> mdrun -v -tablep tablep1.xvg tablep2.xvg -tablea tablea.xvg -deffnm md
>
> How Gromacs know which potential belong to which bond? Isnt it easier to fit
> the curve into the parabolic shape and extract both equilibrium
> distance/angle and the force constant adding to ffbonded.itp ?
Gromacs has a naming scheme for its tables.
For bonded tables:
<TRUNC>_<A,B or D><NR>.xvg
and for non-bonded tables:
<TRUNC>_<E1><_E2>.xvg
TRUNC is determined by the -table (nonbonded) and -tableb (bonded) options.
E1,E2 are energy groups
A,B,D stands for angle, bond, dihedral
NR is the integer you specify in 4th column for of the bonds or angles
block in the top file.
For example
[ angles ]
; ai aj ak funct NR k
1 2 3 8 1 1.0
(k ist another scale factor)
I normally just use the default naming convention (mdrun without
-table options), which lead to table names like
table_A_B.xvg, table_b1.xvg and table_b1.xvg.
Christoph
>
> I am sorry for basic questions but it is not clear to me.
>
> Thanks,
>
>
> Steven
>
>
>
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>
--
Christoph Junghans
Web: http://www.compphys.de
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