wang kelvin wrote:
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 .
Thanks for the detailed description - it sounds like a classic case of
normal behaviour under periodic boundary conditions :-) Check out
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
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 .
Maybe it was just done for gmx for efficiency with constraint
algorithms, but I'm fairly sure I read about it in a paper for some DMSO
model.
Mark
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