[gmx-users] creating a bilayer of dppc

[Igor Marques]

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


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> 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>* 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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