Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids.
James 2012/10/4 Felipe Pineda, PhD <luis.pinedadecas...@lnu.se>: > To generate starting (non-equilibrated) bilayer structures for use in MD > simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. > Otherwise, for conventional lipids CHARMM-GUI membrane builder > (http://www.charmm-gui.org/?doc=input/membrane). > > Hope it helps! > > Felipe > > > On 10/04/2012 07:46 AM, James Starlight wrote: >> >> Justin, >> >> >> lastly, is there any other ways to obtain bilayers of desired >> dimensions started from just one lipid oriented in desired way for >> instance? >> >> >> James >> >> 2012/10/3, Justin Lemkul <jalem...@vt.edu>: >>> >>> >>> On 10/3/12 12:38 PM, James Starlight wrote: >>>> >>>> Justin, >>>> >>>> thanks for advises. >>>> >>>> Finally how I could effectively reduce size of my system (in x and y ) >>>> to the defined pbc box size ( see picture to the previous comment) ? >>>> >>>> I've noticed that increasing of x and y to the 12 nm I obtain ideal >>>> shape of the bilayer without miss-matches of the left and right sizes. >>>> But when I try to decrease dimensions of that system from 12 to 8 nm >>>> >>>> genbox -cs xz.gro -box 8.04542 8.04542 10.19156 >>>> >>>> I've obtained the system with the broadered water layers again ( as in >>>> the picture which I've shown). >>>> >>> My advice is still the same - you need box vectors that are compatible >>> with >>> both >>> a sensible water layer and membrane leaflets. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> 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 -- 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