[gmx-users] clear orientation during MD

[David van der Spoel]

Rongliang Wu wrote:
> 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.

How about other periodicity effects?
Do you have separate coupling groups for decane and water? Otherwise the 
decane might freeze.

> 
> Thanks in advance!
> 
> Regards!
>                     
> Sincerely,
> 
> 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
> 　　　　　　　　　　2005-12-16
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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