<div class="gmail_quote"><div>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.<br>
<br>Please also see the paper of Skaf (it seems of 1997) for DMSO force field...<br><br><br>Vitaly<br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Hi everybody,<br>
<br>
I am currently doing MD simulations with Gromacs-4.0.2 (ffG45a3) using<br>
dmso as solvent.<br>
While checking the topology dmso.itp, which is given in<br>
/gromacs-4.0.2/share/gromacs/top, I have noticed some inconsistencies<br>
compared to the default parameters for dmso given in ffG45a3bon.itp:<br>
<br>
[ atoms ] ; nr type ...................<br>
1 SDMSO .............<br>
2 CDMSO .........<br>
3 ODMSO .....<br>
4 CDMSO ...<br>
<br>
_<br>
###dmso.itp:###_<br>
<br>
[ bonds ]<br>
; ai aj funct b0 kb<br>
1 2 1 0.195 376560 ; kb from Methionine<br>
1 3 1 0.153 502080 ; kb from C=O bond<br>
1 4 1 0.195 376560<br>
<br>
<br>
_###according to ffG45a3bon.itp:###<br>
<br>
_[ bonds ]<br>
; ai aj funct b0 kb<br>
1 2 1 0.195 4.9500e+06 ; gb_39<br>
1 3 1 0.153 8.0400e+06 ; gb_38<br>
1 4 1 0.195 4.9500e+06 ; gb_39<br>
<br>
<br>
Obviously the corresponding values of kb differ by one order of<br>
magnitude (105 vs. 106). Is it possible that the dmso.itp is sort of<br>
out-dated? Does anyone hav any experience with this and can recommend a<br>
parameter set?<br>
<br>
ffG45a3bon also provides some additional parameters for "virtual" bonds<br>
in the dmso molecule which are completely neglected in the existing<br>
dmso.itp (gb_44, gb_45). Since the tetrahedral surroundings of the<br>
sulfur atom are already fixed by means of the dihedral angle gi_2, are<br>
these additional bonds in your opinion really necessary? In some<br>
simulations they seem to cause some trouble with the lincs algorithm...<br>
<br>
Well, it would be very kind if anyone could give me a little help with<br>
the problems depicted above.<br>
</blockquote></div><br clear="all"><br>