Dear all!
Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? James 2012/5/28 Jon Kapla <jon.ka...@mmk.su.se> > Hi, > > The easiest solution is probably to write a script that reorders the > structure file (gro for example, just swap the lines in each lipid, and use > "editconf -f file.gro -resnr 1" to renumber) the way it is written in the > topology. > > Cheers > Jon > > > On 2012-05-28 08:03, James Starlight wrote: > > Peter, > > Thanks for advise. > > I've found already pre-equilibrated POPC bilayers with 200 lipids. I've > examined that lipids and found that they are very similar to the berger's > lipids (it consists of equal nymber of atoms ) but the atom order in each > lipid is slightly different than in Tieleman's popc.itp file so during > processing of that lipids I've got error of non-matching atoms. Is there > any trivial way to make new popc.itp based on existing gro file with > correct atom order ? > > > James > > 2012/5/26 Peter C. Lai <p...@uab.edu> > >> 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@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-requ...@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 >> p...@uab.edu | Birmingham AL 35294-4461 >> (205) 690-0808 | >> ================================================================== >> >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > > -- > _____________________________________________________ > > Jon Kapla > Division of Physical Chemistry > Dpt. of Materials and Environmental Chemistry (MMK) > Arrhenius Laboratory > Stockholm University > SE-106 91 Stockholm > Pos: PhD Student > Phone: +46 8 16 11 79 (office) > Phone: +46 70 304 19 89 (cell) > E-mail: jon.ka...@mmk.su.se > _____________________________________________________ > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists