2006/6/28, 이 선주 <[EMAIL PROTECTED]>:
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.
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
