Justin,
I don't need the files. I'm just trying to save you time. If I want to see > a coordinate file, I'll ask for it to be sent to me directly. I have seen > no such need yet. Ok. > Application of pressure causes the box to change. The water won't leak in > during NVT because the components of the system are trying to keep the box > full since its dimensions are invariant. Such leakage is typical during > equilibration, as I've said. You should not be alarmed by this result. So presence of several water molecules within the membrane after equilibration will not cause futher errors in simulation, won't it? After 1 ns MD simulation of my system I've found that some waters were excluded from the bi-layer. By the way the system prepared by G_membed consisted of more water molecules within the membrane after solvation via Genbox ( I've used vdv radius of 0.5 for carbons ). Finally, I'd like to analyse results obtained after 1ns simulation. Firstly I want to compare some physical values of my system with the experiment. I found that I can analyse some such parametries like A per lipid ( I've already known this experimental value) as well as *Density of the Membrane and the coefficent of the **Lateral Diffusion for Lipids. Where I could found last two experimental values for my system as well for other lipids? James * > > -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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