[gmx-users] Supradiffusivity

이 선주 sunnytov at hotmail.com
Wed Jun 28 19:52:20 CEST 2006


Hello Users

I have seen that it is needed to define three separate groups for 
center-of-mass motion removal: water and a separate group for each lipid 
layer in order to remove supradiffusivity of the two leaflets.

Can anyone tell me whether my settings are correct?

-----------------------------------------------------------------------------

comm-grps                = UpLeaflet LowLeaflet SOL
nstxout                  = 1000
nstvout                  = 1000
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 1000
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.0
coulombtype              = PME
rcoulomb                 = 1.0
rvdw                     = 1.0
Tcoupl                   = Nose-Hoover
tc_grps                  = UpLeafelt  LowLeaflet   SOL
tau_t                    =           0.5           0.5            0.5
ref_t                    =  303  303  303
----------------------------------------------------------------------------

Is it correct or enough to remove supradiffusivity and calculate diffusion 
coefficient? 

Thanks in advance
Sunjoo





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