[gmx-users] Re: Unequal water of Bilayer system in *PR step
sudheer.pbm07 at gmail.com
Fri Sep 26 14:41:15 CEST 2008
>> > Hi Users,
> >> > I have extended the lipid bilayer(popc) from default
> >> popc128a.pdb to
> >> > 200 popc molecules with suffcient water by using genbox.
> >> > genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9,
> >> to the
> >> > out.gro(contain 200 popc) minimisation ran fine later swtich over
> >> to *PR
> >> > with fc-1000 on P8,C51,C53 of popc and saw output_pr.gro in VMD
> >> water has
> >> > weird strcuture(up side downs but popc structure is quite fine).
> >> > So I have reduced the pbc box size to 9 9 6.7 with *editconf
> >> later I ran
> >> > minimsation and *PR, "now water" and POPC structures are "fine"
> but I
> >> > observed "unequal water".
> >> What do you mean with "unequal water"?
> >> Thanks for the response unequal water means ' when I noticed the
> >> intial 200popc.gro use VMD water molecules present bothsides almost same
> >> towards corners of the simulation box and centre of the above and below
> >> popc heads but after *PR one side of the leaflet bilayer corners have
> >> very less water (say 20 water molecules earlier 80 water molecules)
> >> looks at corners doesnt have water seems. I hope you understood my
> > Probably your system isn't perfectly centered within the box and you are
> >seeing "diffusion" from PBC.
> It is however not totally clear (to me) what is the problem. If it is a
> change of water density in a particular area of the simulation box, it
> well be that the water distribution was not so "ideal" in your starting
Justin suggestion "run a bit longer" is good. especially that you have not
> given us much information on that!
Thanks for the replies, I have run only 500ps *PR step and attaching
title = popc restrained
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 250000 ; total 500 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
pbc = xyz
; Berendsen temperature coupling is on in two groups
Tcoupl = Berendsen
tc-grps = POPC SOL
tau_t = 0.1 0.1
ref_t = 323 323
; Anisotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 2.0 2.0 2.0 0 0 0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0 0
; Energy monitoring
energygrps = POPC SOL
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 323.0
gen_seed = 173529
Could you suggest me if any wrong in this pr.mdp file, may be this is
As both of you said simulate bit longer, if yes will it cause equal
distribution of water?
Thanks in advance.
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