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

[Catarina A. Carvalheda dos Santos]

Priya,

Did you perform at least one energy minimization step before that? Because
you should, one or several, to remove unfavorable interactions.

On 19 November 2014 11:05, Priya Das <priyadas001 at gmail.com> wrote:

> 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
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biophysics Group
College of Life Sciences, University of Dundee
Dundee, DD1 5EH, Scotland, UK