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

[Xavier Periole]

On Fri, 26 Sep 2008 18:11:15 +0530
  "sudheer babu" <sudheer.pbm07 at gmail.com> wrote:
>>>      > 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 ...

-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------