Thanks, Justin I'll test your program soon. Today also I have some problems with generation of the posre for lipids
I have lipid bilayer in pdb. Then I selected one lipid molecule and move it to separate pdb and convert it to gro via editconf. Than I've used genres and generate posre file for 1 lipid. Than I include tis posre to topology of my bilayer using gropt I obtain eror that I'm using wrong posre topology Also I've tried to include posre.itp to my lipid.itp ( this file contain link to posre on default) This run didnt produce any errors but as the result posres have not been worked ( I obtained perturbed bilayer after minimization) How I can generate work posre for my bilayer to prevent perturbation after equilibration or minimization ? James 2011/10/31 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> >> In some papers I found Gromacs graphs showed indirectly measurements of >> the time evolution of the Area per lipid value. What gromac's program could >> be used for it for cheacking the above value during simulation runs ? >> >> > There is no Gromacs tool for this. For a simple membrane system, one can > use g_energy to extract box vectors over time, which can then be divided by > the number of lipids per leaflet to extract the APL. For systems with > proteins embedded in membranes, it is no trivial exercise to make such > measurements. We wrote a program several years ago that calculates APL for > such systems: > > http://www.bevanlab.biochem.**vt.edu/GridMAT-MD/<http://www.bevanlab.biochem.vt.edu/GridMAT-MD/> > > The program can only be run on single snapshots at the moment, but you can > assemble time evolution from the output. > > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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