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: [email protected] [mailto:[email protected]] 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. > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _______________________________________________________________________ !!!! new E-mail address: [email protected] !!!! 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
