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

2017-06-17 Thread 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

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

2017-06-17 Thread 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