Hey
Rakhee
Since, I have never used VOTCA to do bonded potential coarse-graining
along with non-bonded interactions, my suggestions may be incomplete.
So I request other experienced members of the group to complete
my suggestions or correct me if I made any mistake.
I suggest the following steps,
1. Compute target RDFs and potential of mean forces from your
AMBER simulations.
2. Invert PMFs to get CG bonded interactions.
3. Then you need to do IBI coarse-graining of non-bonded interactions
For that you need to create some GROMACS specific files. These are
mainly
1. initial CG configuration file specified as *.gro
2. Topology file *.top specifying CG bonded and nonbonded
interaction settings
3. MD simulation parameter file specified as *.mdp
4. the default table.xvg file
you should go through tutorial files of votca to get an idea about how
these files
look and go through gromacs manual. Information about how to set up
user specified tabulated
potentials in gromacs can be found at
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Since, I have not worked with AMBER suite, i am not sure whether it is
possible to directly
convert from AMBER format files to GROMACS files. Efforts required to
generate GROMACS specific files for coarse-graining would depend upon
the complexity of your reference system.
Or alternative would be to set up your reference simulations itself in the
GROMACS and then use
standard VOTCA tools to do mapping n stuff.
This option, I guess would require similar efforts as in generating CG set
up files.
cheers
sikandar
On Wed, Feb 8, 2012 at 12:11 PM, rp <[email protected]> wrote:
> Dear Votca Users,
>
> I have my atomistic simulations done in using AMBER MD suite. In the
> Votca manual this mention on use of GROMACS trajectory and input
> file.
> I want derive the non bonded potentials using iterative Boltzmann
> inversion and bonded interactions using potential of mean force of
> the
> CG degrees of freedom. Can anyone give me some more information on the
> input files required for the procedure or where I can find some
> related examples.
> Can I work with the parameter and coordinate files used by AMBER.
>
> Thanks for suggestions
> Rakhee
>
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