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 <[email protected]
<mailto:[email protected]>> 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 /<[email protected]
<mailto:[email protected]>>/* wrote:
From: Justin A. Lemkul <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] Instantaneous Square Displacement
To: "Discussion list for GROMACS users" <[email protected]
<mailto:[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 <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
========================================
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