dear delara,<br><br>converting the monolayer gro to pdb with editconf and then using that pdb in packmol might be a way of doing it.<br><br>don't forget to adjust your *top file to the new number of items (2x) and their order.<br>
<br>that should do it, i guess<br><br><br>best regards,<br>igor<br><br><br><br><br clear="all"> Igor Marques<br> <a href="http://molecular-modeling.dq.ua.pt/">http://molecular-modeling.dq.ua.pt/</a><br>
<br><br><div class="gmail_quote">On Wed, Mar 9, 2011 at 11:16 AM, delara aghaie <span dir="ltr"><<a href="mailto:d_aghaie@yahoo.com">d_aghaie@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font:inherit" valign="top"><div><b>Dear gromacs users</b></div>
<div><b>having the .gro file for the dppc monolayer, how can i create a bilayer?</b></div>
<div><b>I am interested in making bilayer from the equilibrated monolayer which i have for dppc.</b></div>
<div><b>what changes are necessary to be done in simulation files to start a run with the bilayer?</b></div>
<div><b>Thanks for your time</b></div>
<div><b>D.M<br></b><br>--- On <b>Tue, 3/8/11, Justin A. Lemkul <i><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></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 <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] Instantaneous Square Displacement<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Date: Tuesday, March 8, 2011, 2:57 PM<br><br>
<div><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]<a href="http://vt.edu" target="_blank">vt.edu</a> | (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>
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