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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