[gmx-users] creating a bilayer of dppc

[Justin A. Lemkul]

Igor Marques wrote:
> dear delara,
> 
> converting the monolayer gro to pdb with editconf and then using that 
> pdb in packmol might be a way of doing it.
> 
> don't forget to adjust your *top file to the new number of items (2x)  
> and their order.
> 
> that should do it, i guess
> 

That might work, or simply:

1. Rotate the existing monolayer by 180 and translate suitably with editconf
2. Position both monolayers in a box (also editconf)
3. Concatenate the two coordinate files.

-Justin

> 
> best regards,
> igor
> 
> 
> 
> 
>       Igor Marques
>       http://molecular-modeling.dq.ua.pt/
> 
> 
> On Wed, Mar 9, 2011 at 11:16 AM, delara aghaie <d_aghaie at yahoo.com 
> <mailto:d_aghaie at yahoo.com>> wrote:
> 
>     *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
>     <mailto:jalemkul at vt.edu>>/* wrote:
> 
> 
>         From: Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>         Subject: Re: [gmx-users] Instantaneous Square Displacement
>         To: "Discussion list for GROMACS users" <gmx-users at gromacs.org
>         <mailto: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 <http://vt.edu> | (540) 231-9080
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

========================================