[gmx-users] co-solvent topologies (G53a?)

[Nuno R. L. Ferreira]

----- Original Message ----- 
From: "Alessandra Villa" <villa at theochem.uni-frankfurt.de>
To: <gmx-users at gromacs.org>
Sent: Friday, October 22, 2004 9:18 AM
Subject: Re: [gmx-users] co-solvent topologies (G53a?)


>
> >
> > Hi
> >
> > Does anybody have Gromos (G53a?) .itp topology files for methanol
(Walser
> > et. al, JCP 2000) and DMSO (Geerke et al., JPC-B 2004)?
> >
> > Tryed to build those files, but I have doubts that they are ok.
>
> Both the topologies can be deduced from the ffG53a...  rtp file.

Hi Dr Villa

We meet again ;)
I deduced the topologies that way, but I was uncertain about some entries in
the bonds/angles/dihedrals fields.  Namely, in the ffG53a?, there's a a
gb_49 (ODsmo - CDmso) and gb_50 (CDmso - CDsmo), that aren't used in the
topology you kindly provided me.  Guess is used for another DMSO model.

Anyway, thanks.
Nuno

P.S. Just noticed that the methanol model uploaded in the gmx contribs. page
by C. Freudenberg, is based in Walser et. al, JCP 2000.  I found a ga_47
(HMet-OMet-CMet), but I didn't find out in the article any reference to this
angle.  So, Freudenberg's model still holds.


> Anyway hereby I send you the top file of DMSO that I have (Geerke et al.,
> JPC-B 2004). I do not have anymore
> The topology of methanol (Walser et. al, JCP 2000).
>
> kind regards
>
> Alessandra
>
> *****
> #include "ffG53a5.itp" ; or "ffG53a6.itp"
>
> [ moleculetype ]
> ; name  nrexcl
> DMSO 2
>
> [ atoms ]
> ;   nr    type   resnr  residu  atom    cgnr    charge
>      1     SDMSO     1   DMSO    SD      1        0.12753 32.06000
>      2     CDMSO     1   DMSO    CD1     1        0.16  15.03500
>      3     ODMSO     1   DMSO    OD      1       -0.44753   15.99940
>      4     CDMSO     1   DMSO    CD2     1        0.16    15.03500
>
> [ bonds ]
> ;  ai    aj funct          b0       kb
>      1     2     2       0.1937991  4.9500e+06
>      1     3     2       0.153    8.0400e+06
>      1     4     2       0.1937991 4.9500e+06
>
> [ angles ]
> ;  ai    aj    ak   funct        theta       kt
> 3       1       2       2       106.75  503.0
> 3       1       4       2       106.75  503.0
> 2       1       4       2        97.40  469.0
>
> [ dihedrals ]
> ;  ai  aj      ak      al   funct     xi         kxi
> 1       2       4       3       2 35.264     334.720    ; default params
>
> [ system ]
> DMSO
>
> [ molecules ]
> DMSO 208
>
>
> ****
>
>
>
>
>
>
>
>
>
> >
> > Regards,
> > Nuno
> >
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>