[gmx-users] Building different size membranes using gromacs 5.1.4

Kevin Boyd kevin.boyd at uconn.edu
Fri Aug 9 05:22:00 CEST 2019


Note that the solution Dallas suggested will work (along with changing the
resulting box dimensions), but that it may lead to clashes at periodic
boundaries. You may need to re-minimize (perhaps with soft-core potentials
if there are serious clashes) and re-equilibrate, which would probably
defeat the purpose of starting from a pre-equilibrated structure. It's a
lot easier to duplicate a bilayer than it is to shrink it.

Consider using a server/tool to generate a system for you instead, such as
the CHARMM-GUI.

Kevin

On Thu, Aug 8, 2019 at 8:00 PM Dallas Warren <dallas.warren at monash.edu>
wrote:

> Select molecules within the appropriate x y coordinates (if that is the
> plane that the membrane is in) that will provide that number of molecules,
>
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> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Fri, 9 Aug 2019 at 02:57, Pradeepa Kumari <pradeepakumari94 at gmail.com>
> wrote:
>
> > I want to extract 128 DPPC bilayer section(1/4) from pre-equilibrdated
> 512
> > DPPC bilayer.How can I do this with gromacs 5.1.4? Any assistance you can
> > provide would be greatly appreciated.
> >
> > Thanking you in advance.
> >
> > Regards,
> > dananjana
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