[gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation

[Sajeewa Pemasinghe]

Hi all,

I have to carry out MD simulations involving PEG 6000 molecules. When I
first build this it is a very long (~480 Angstrom) linear chain. I have the
bond/angle/dihedral parameters for this linear structure. Usually when I
introduce a non-standard residue, I perform an optimization in Gaussian and
then get the parameters and create an itp file with those parameters. In
this case as the molecule is too big I cannot go for a quantum
optimization.

1) Should I put this in a box of water and let it equilibrate and get the
parameters for the equilibrated structure? But that box would then be huge
at the beginning because at the beginning the structure is linear(Is there
a way out of this?).  This must be quite a naive question. But could you
give me your suggestions as  to what path I should follow?

2) I came across this link .
http://www.gromacs.org/Documentation/How-tos/Polymers

So should I create separate rtp files for the above three fragments? Or
should I go with creating an itp file and include that string in the .top
file?

I really appreciate your help on this.

Thank you

Sajeewa