[gmx-users] Supradiffusivity

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

2006/6/28, 이 선주 <sunnytov at hotmail.com>:

> 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?


Yes, they seem correct. However, I don`t know if you have to use the same
groups for the temperature coupling...



>
> -----------------------------------------------------------------------------
>
> 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?


I think so, but beware of the time scales. Check the literature.

Regards.

Pedro.





>
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