[gmx-users] Re: Creating a monolayer from Martini bilayer

[Tsjerk Wassenaar]

Hi Neha,

You can use trjconv with option -pbc mol to put all molecules in the box.
If you want a vacuum, you probably don't want to add more water. But just
play with it and see what comes out. CG simulations are fast enough for
that kind of trial-and-error.

Cheers,

Tsjerk


On Mon, Jun 3, 2013 at 8:26 PM, Neha <nshafique at wesleyan.edu> wrote:

> Hi Tsjerk,
>
> Thank you so much for being so patient!
> I have yet another question. The membrane I got from the Martini website
> already has water in it. Do I need to add more water and if so why?
>
> Also how exactly do I use trjconv to put all molecules in the box? Sorry
> for
> being so annoying need a lot of elaboration!
>
>
> Tsjerk Wassenaar wrote
> > Hi Neha,
> >
> > A single structure is like a trajectory with only one frame :p trjconv
> > works on those as well.
> > Right, set the center at 0,0,0 and choose the lipids as group for
> > centering.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Mon, Jun 3, 2013 at 7:31 PM, Neha &lt;
>
> > nshafique@
>
> > &gt; wrote:
> >
> >> Hi, thank you so much!
> >>
> >> This way seems promising, however I am not sure how to center the
> bilayer
> >> around z=0. I thought I could use editconf but I might be confused as to
> >> how
> >> Gromacs centers its objects. If I put -center 0 0 0 does that mean the
> >> bilayer is centered around z = 0?
> >>
> >> Also I thought that trjconv only dealt with trajectory files. What I
> have
> >> right now is a structure file, a topology file and an map file. After I
> >> have
> >> solvated, I will still only have a new structure file, so what would the
> >> trjconv be acting on?
> >>
> >> Thank you so much for helping out a newbie!
> >>
> >>
> >> Hey :)
> >>
> >> Just center the bilayer around z=0, solvate and put all molecules in the
> >> box with trjconv. Then add 10 to the PBC Z-component (third number from
> >> the
> >> last line in the .gro file).
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >>
> >>
> >>
> >>
> >> --
> >> View this message in context:
> >>
> http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008747.html
> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> >> --
> >> gmx-users mailing list
>
> > gmx-users@
>
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to
>
> > gmx-users-request@
>
> > .
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > gmx-users mailing list
>
> > gmx-users@
>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to
>
> > gmx-users-request@
>
> > .
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008751.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.