[gmx-users] Coordinate file for lipid bilayer

[Peter C. Lai]

Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0
Tieleman's lipids require you to generate a dummy tpr for use with trjconv
to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro
-pbc mol -ur compact) first.

Lots of people have their own bilayer but they may be for different FFs
which means the atom naming would not be immediately be compatible with
your FF; for example mine are built for charmm36 and would require atom
renaming for another FF, even charmm27.

On 2012-05-26 11:24:12AM +0400, James Starlight wrote:
> Dear Gromacs Users!
> 
> 
> I want to perform MD simulation of my membrane protein in POPC or POPE
> bilayer using Tieleman's parameters for lipids by means of gromos united
> atom force field. The main problem is that the pre-equilibrated bilayers
> wich I found on the Dr. Tieleman's site consist of no more that 128 lipids
> but I want to simulate my protein with bigger number of lipids ( for
> example starting from 200 lipids ).
>  What should I do in that case ?  Could you provide me with  some tools for
> construction of such united-atoms bilayers with desired dimensions ?
> Finally is there any others pre-equilibrated bilayers aviable for
> downloading besides Dr. Tieleman's site ?
> 
> 
> thanks for your help,
> 
> James S.

> -- 
> 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


-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================