[gmx-users] about DMSO c-c bond and c-o bond in ffg53a6 force field

[Mark Abraham]

wang kelvin wrote:
> Hi, everyone.
> 
> I am simulating DMSO. At fisrst ,bond parameters contain two c-c 
> bonds,and c-o bond ,which actually not in existence. But gmx 's force 
> field ffg53a6 documents in top directory defines these bonds. When 
> running mdrun , system reminds "segmentation default". then i get these 
> virtual bond away , since that mdrun is ok !
> 
> Can anyone tell me why gmx define these bonds (ie. C-O bond ,C-C bond)? 
> And has eliminating these bonds effects on simulating result?
> 
>  
> 
> Any suggestion is appreciated.

I'd suggest describing your observations more coherently and in more detail.

Otherwise, with a view to using SHAKE, some united-atom DMSO models 
prefer to define six bonded interactions, rather than three bonded 
interactions and three angle interactions. Thus, DMSO C-C and C-O 
interactions can exist. However, you should already know about this from 
reading the literature about your DMSO model, right? :-)

Mark