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

[Kevin Boyd]

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,
>
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fcurrent%2Fonlinehelp%2Fselections.html&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119064029&amp;sdata=FT9iErLytB6N7jLMlEa0ITbjb2OJkKCQ6sv1HN9kZRQ%3D&amp;reserved=0
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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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