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 <[email protected]> wrote: From: Justin A. Lemkul <[email protected]> Subject: Re: [gmx-users] Instantaneous Square Displacement To: "Discussion list for GROMACS users" <[email protected]> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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