[gmx-users] Coordinate file for lipid bilayer
Peter C. Lai
pcl at uab.edu
Sat May 26 13:04:11 CEST 2012
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.
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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 |
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