dear delara, converting the monolayer gro to pdb with editconf and then using that pdb in packmol might be a way of doing it.
don't forget to adjust your *top file to the new number of items (2x) and their order. that should do it, i guess best regards, igor Igor Marques http://molecular-modeling.dq.ua.pt/ On Wed, Mar 9, 2011 at 11:16 AM, delara aghaie <d_agh...@yahoo.com> wrote: > *Dear gromacs users* > *having the .gro file for the dppc monolayer, how can i create a bilayer?* > *I am interested in making bilayer from the equilibrated monolayer which i > have for dppc.* > *what changes are necessary to be done in simulation files to start a run > with the bilayer?* > *Thanks for your time* > *D.M > * > --- On *Tue, 3/8/11, Justin A. Lemkul <jalem...@vt.edu>* wrote: > > > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Instantaneous Square Displacement > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Tuesday, March 8, 2011, 2:57 PM > > > > Mark Abraham wrote: > > On 8/03/2011 3:01 AM, Jennifer Williams wrote: > >> > >> Hi, > >> > >> I am writing a paper where I describe that gas molecules move inside a > pore and then stick for long periods of time in occlusions in the pore wall. > >> > >> A reviewer has mentioned that I could illustrate this effect by using > "instantaneous square-displacement". > >> > >> I have already produced MSD vs time plots and used them to obtain the > self diffusion coefficient. Can someone shed some light on how I can obtain > the instantaneous square displacement in gromacs? > > > > I have no idea what "ISD" means, and Google doesn't know either :) > Perhaps they want to see the diffusion of a single molecule? > > > > Searching for "instantaneous square displacement" turns up very little (3 > results), but the last seems to be what you need, as long as this person is > correct: > > > http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1 > > Section 2.3.3. > > -Justin > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://us.mc1301.mail.yahoo.com/mc/compose?to=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<http://us.mc1301.mail.yahoo.com/mc/compose?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