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

[Justin Lemkul]

On 6/17/17 8:55 AM, Sajeewa Pemasinghe wrote:
> 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?
> 

A polymer is just a chain of repeating units.  You should not attempt to 
optimize/parametrize an entire polymer, because you will get 
conformation-specific parameters that are likely to be unphysical.  If 
parameters do not already exist (I find it unlikely that nobody has simulated 
PEG before), you can easily parametrize the ethylene glycol units by optimizing 
monomers and dimers to get charges and bonded parameters.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================