<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><STRONG>Dear gromacs users</STRONG></DIV>
<DIV><STRONG>having the .gro file for the dppc monolayer, how can i create a bilayer?</STRONG></DIV>
<DIV><STRONG>I am interested in making bilayer from the equilibrated monolayer which i have for dppc.</STRONG></DIV>
<DIV><STRONG>what changes are necessary to be done in simulation files to start a run with the bilayer?</STRONG></DIV>
<DIV><STRONG>Thanks for your time</STRONG></DIV>
<DIV><STRONG>D.M<BR></STRONG><BR>--- On <B>Tue, 3/8/11, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] Instantaneous Square Displacement<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Tuesday, March 8, 2011, 2:57 PM<BR><BR>
<DIV class=plainMail><BR><BR>Mark Abraham wrote:<BR>> On 8/03/2011 3:01 AM, Jennifer Williams wrote:<BR>>> <BR>>> Hi,<BR>>> <BR>>> 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.<BR>>> <BR>>> A reviewer has mentioned that I could illustrate this effect by using "instantaneous square-displacement".<BR>>> <BR>>> 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?<BR>> <BR>> I have no idea what "ISD" means, and Google doesn't know either :) Perhaps they want to see the diffusion of a single molecule?<BR>> <BR><BR>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:<BR><BR><A href="http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1" target=_blank>http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1</A><BR><BR>Section 2.3.3.<BR><BR>-Justin<BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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