[gmx-users] clear orientation during MD

Rongliang Wu wurl04 at iccas.ac.cn
Fri Dec 16 09:56:00 CET 2005

Hello gmx-users,

	  my system is a interface of water and decane and after MD i can see clearly that most of the decane molecules orientate in the x direction. i have read a literature by David van der Spoel in which he talked about formation of orientated water under large cutoffs. myparameters are:
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.0
coulombtype              = PME
rcoulomb                 = 1.3
rvdw                     = 1.0
tcoupl                   = Berendsen
tc-grps                  = system
tau_t                    = 0.1
ref_t                    = 300
Pcoupl                   = Berendsen
Pcoupltype               = semiisotropic
tau_p                    = 1.0
compressibility          = 4.5e-5 0
ref_p                    = 1.0 1.0 

why? are there any problems with my cutoffs? i have also met with the same problem with a single system of heptadecane with 
coulombtype              = reaction field
Pcoupltype               = isotropic
it's wierd but David said in his article that these two methods merely generate such problems.

Thanks in advance!


Rongliang Wu
State Key Laboratory
of Polymer Physics and Chemistry
Center of Molecular Science
Institute of Chemistry
Chinese Academy of Sciences

          wurl04 at iccas.ac.cn

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