[gmx-users] creating a bilayer of dppc

[delara aghaie]

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 <jalemkul at vt.edu> wrote:


From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Instantaneous Square Displacement
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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

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