[gmx-users] Re: dmso topology

[Vitaly V. Chaban]

I used the DMSO model from dmso.itp for some test runs with the gromacs
versions before 4.0 and it gave me the same diffusion constant (~1.1) as
reported in the original paper. So, the topology seems to be OK in general.

Please also see the paper of Skaf (it seems of 1997) for DMSO force field...


Vitaly



>
> Hi everybody,
>
> I am currently doing MD simulations with Gromacs-4.0.2 (ffG45a3) using
> dmso as solvent.
> While checking the topology dmso.itp, which is given in
> /gromacs-4.0.2/share/gromacs/top, I have noticed some inconsistencies
> compared to the default parameters for dmso given in ffG45a3bon.itp:
>
> [ atoms ]     ;   nr    type          ...................
>   1     SDMSO   .............
>   2     CDMSO   .........
>   3     ODMSO   .....
>   4     CDMSO   ...
>
> _
> ###dmso.itp:###_
>
> [ bonds ]
> ;  ai    aj funct          b0       kb
>   1     2     1     0.195    376560    ; kb from Methionine
>   1     3     1     0.153    502080    ; kb from C=O bond
>   1     4     1     0.195    376560
>
>
> _###according to ffG45a3bon.itp:###
>
> _[ bonds ]
> ;  ai    aj funct          b0       kb
>   1     2     1     0.195    4.9500e+06    ; gb_39
>   1     3     1     0.153    8.0400e+06    ; gb_38
>   1     4     1     0.195    4.9500e+06    ; gb_39
>
>
> Obviously the corresponding values of kb differ by one order of
> magnitude (105 vs. 106). Is it possible that the dmso.itp is sort of
> out-dated? Does anyone hav any experience with this and can recommend a
> parameter set?
>
> ffG45a3bon also provides some additional parameters for "virtual" bonds
> in the dmso molecule which are completely neglected in the existing
> dmso.itp (gb_44, gb_45). Since the tetrahedral surroundings of the
> sulfur atom are already fixed by means of the dihedral angle gi_2, are
> these additional bonds in your opinion really necessary? In some
> simulations they seem to cause some trouble with the lincs algorithm...
>
> Well, it would be very kind if anyone could give me a little help with
> the problems depicted above.
>
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