[gmx-users] Hi all

[Mark Abraham]

ann rose wrote:
> Hi
> 
> I am new to Gromacs.
> I would like to simulate oligoether branched polysiloxanes in gromacs. I 
> have the force field availble for the same
> Whether gromacs will support force filed for polymers containing hetreo 
> atmos like silicon?

Yes - this information is part of the force field.

> If so how can I incoroprate this into gromacs?

You will need a thorough working knowledge of at least chapter 5 of the 
manual, and plenty from earlier sections. This will also let you assess 
whether the range of functions computed by gromacs is suitable for your 
forcefield.

> and also
> How to get the starting configuration for the poysiloxanes? ( like .gro, 
> .top, .itp files)

.gro files are structure files... you're responsible for generating 
them. Search the mailing list for suggestions.

.top files can be generated by pdb2gmx if you can generate suitable .rtp 
monomers, but life may be messy here for branched polymers... you may 
need to make these by hand.

.itp files are included by .top files and include your basic force field 
files as well as regularly recycled units like solvents... you need to 
make these.

Mark