[gmx-users] UA simulation of PEO melt

patrick fuchs patrick.fuchs at univ-paris-diderot.fr
Tue May 12 15:54:22 CEST 2009

Hi Zuzana,
I'm actually working on the paramaterization of polyethers with the 
GROMOS developers. Currently in G53a?, there's no such torsion O-C-C-O 
in GROMOS and I don't advice to use any combination of existing 
monoethers. I could figure out that they give the wrong free energy of 
hydration. I hope to have the parameters ready before the end of the 
year. Meanwhile, you can use the recently optimized parameters for 
CHARMM (http://dx.doi.org/10.1529/biophysj.108.133025) though they are 


Zuzana Benkova a écrit :
> Dear GROMACS users
> I  want to run simulations of polyethyleneoxide melt. In literature I 
> have found united atoms force fields that performed well for this kind 
> of simulation. For dihedral potential I need to extend the 
> Ryckaert-Bellemans potential up to the order of six. I have looked at 
> the mailing list and found some information which give advice to change 
> the code for this kind of potential. But I could not figure out where to 
> do this changes and how to do them. I would need some detail to do it. I 
> do not have experience with something like this.
> My second question also concerns PEO. I tried to use GROMOS force field 
> as well for simulations. I used the parameters from ffG53a5 files. In 
> ffG53a5bon.itp I am not sure which code of dihedrals sould be used for 
> C-C-O-C and O-C-C-O and which one for the bond angles. In the case of 
> bond angle I found type ga_8 as suitable, but it seems me from the 
> description that it sould be the same for all three bonds in PEO. This 
> seems to be not OK, since the bending of C-O-C angle is characterized by 
> larger bending constant.
> I would appreciate any help. Thank you in advance
> Zuzana.
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!!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31
Web Site: http://www.dsimb.inserm.fr/~fuchs

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