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
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