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

[wang kelvin]

Thanks MARK for your reply,and your suggestion is very helpful.



I don't write back until mdrun ends just now.

I want to simulate DMSO property as it is cooled. So I put 500 DMSO
moleculers in a box. Ref_t =300  ref_P=1.

During the first 60ps ,the 500 DMSO moleculers seems to be diffusing outside
with box getting larger and larger.



Then box size become stable until 290ps from when box get smaller and
smaller, DMSO meoleculers form several clusters. Gradually clusters get
bigger and bigger ,at last there are three big moleculer blocks in box with
two relatively smaller blocks.



During 1000 -1300ps,big moleculer continue gathering and form two main
blocks ,one is in the upside of the box ,and another is in the underside of
the box. This two blocks' size keep changing ,but the number of blocks never
changed . the whole simulating system has already been stable when 1500ps
comes.



300 K temperature and 1 bar pressure means DMSO is in liquid phase. So I
think DMSO moleculers shoud gather and form relatively big blocks. But I
expect there is only one block in box,and simulation results give two blocks
.



By the way, I have searched many DMSO literaures ,but never seen information
about c-c bond and c-o bonds in gmx force field . maybe I am quite new ,and
not good at English .



Thanks MARK again for your suggestion and kindness.



Your sincerely

Kelvin wang


2008/5/22, Mark Abraham <Mark.Abraham at anu.edu.au>:
>
> 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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