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 [email protected] > 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 [email protected]. > 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 [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
