[gmx-users] UA simulation of PEO melt

[Zuzana Benkova]

Hi Patrick,
Thank you very much for your response. I have just downloaded the paper of
which you sent the reference. I have not found other FF parameters except
for the torsional one about the C-C bond. I have also some papers which
provide good results on PEO simulations (JCP, 124, 234901 (2006); JCP, 102,
9725 (1995).) but I am limited with the order of Ryckaert-Bellemans
potential. Unfortunately I do not have any idea how to perform the code
modification to extent the torsional expansion. This was the second part of
my first mail. I hope somebody will provide me with details necessary to
modify the code appropriately and with all the changes associated with that.


Greetings
Zuzana

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of patrick fuchs
Sent: Tuesday, May 12, 2009 3:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] UA simulation of PEO melt

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 
all-atom.
Cheers,

Patrick

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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