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

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Wed Nov 19 11:47:43 CET 2014

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.


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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

Catarina A. Carvalheda

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

More information about the gromacs.org_gmx-users mailing list