[gmx-users] Unequal water of Bilayer system in *PR step

[sudheer babu]

>
> Thank you very much to Xavier for your valuable suggestion
> >>>      > 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
> >> problem,
> >> >>
> >> >
> >> > 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
> >> could
> >> well be that the water distribution was not so "ideal" in your starting
> >> configuration.
> >>
> > 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
> > pr.mdp file
> > 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
> > trivial query
> > As both of you said simulate bit longer, if yes will it cause equal
> > distribution of water?
> > Thanks in advance.
>
> Well nothing obviously wrong in the mdp file.
> It may be time to let the lipids free to move ...
>
>
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