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.
Thanks in advance!
Kind regards
Markus
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