[gmx-users] Replicating and equilibrating DPPC 128 lipid. pdb

[Priya Das]

Dear Catarina,

Thankyou very much for the reply.
I was able to replicate the DPPC membrane structure.
But while equlibration step  using the code :
pbc  = xyz
coulombtype =PME
rcoulomb = 1.0
rvdw = 1.4
tcoupl = Berendsen
tc-grps = System
tau_t = 0.1
ref_t = 325
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 2.0 2.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
constraints = all-bonds

I get LINCS error message.
But if i use NONE option for contsraints, i get results. Is it the right
way of doing it?

On Wed, Nov 19, 2014 at 4:17 PM, Catarina A. Carvalheda dos Santos <
c.a.c.dossantos at dundee.ac.uk> wrote:

> Hi Priya,
>
> You can use genconf with the option -box to replicate your box (in this
> case your membrane) as many times as you want in the x,y and z directions.
> Keep in mind that -box only deals with integers (number of boxes), so
> something like "-box 1.5 2.5 1" will be equivalent to "-box 2 3 1". If the
> system is too large after replication you can always do some scripting and
> "adjust" the final membrane size.
>
> After this, the equilibration of the new membrane has to be done as you
> mentioned (you can follow the same procedure used to equilibrated the
> initial 128 DPPC membrane, for example) and only then you align and insert
> your protein in the membrane. There are several tools available for this
> last step, I would recommend using lambada for the protein alignment and
> inflategro2 for the protein insertion (you can checkthis
> <http://pubs.acs.org/doi/abs/10.1021/ci3000453> reference).
>
> Hope this helps.
>
> Regards,
>
> On 19 November 2014 09:35, Priya Das <priyadas001 at gmail.com> wrote:
>
> > I am working with a transmembrane protein (pentamer). From references i
> > have chosen DPPC 128. pdb as my membrane structure. But as my protein
> size
> > is huge , i need a larger simulation box. Therefore, i need to replicate
> > the DPPC membrane because 4 such DPPC.pdb (128 lipids) forms a large box.
> > After replicating the system has to be equilibrated.
> > Is anyone aware of this process.
> > Please reply.
> >
> > --
> > *Let us all join hands to save our " Mother Earth"*
> > ------------------------------------------------------------------------
> > Regards,
> > Priya Das
> > Research Scholar
> > Dept. of Computational Biology and Bioinformatics,
> > University of Kerala
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>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biophysics Group
> College of Life Sciences, University of Dundee
> Dundee, DD1 5EH, Scotland, UK
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-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala