[gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

[Justin Lemkul]

On 10/10/14 2:02 AM, rama david wrote:
> Dear Friends,
>        I want to do the simulation of lipid membrane with peptides. Peptide
> concist  8 amino acid.I want to keep the two or four peptide just away from
> membrane and
> want to see how they interact with membrane.
>            I choose the DPPC membrane for the work ( from D.Peter Tieleman ).
>   I am following the Justin tutorials for the work flow.
>
>   Problems are  as per follow :
>
>           The size of dppc128.gro is very small on z-axis to put my two or
> four peptide
> ( peptide is made of 8 amino acid). So I want to increase the size of
> dppc128.gro on z axis. so I can put two or four peptide peptide.
>         Please tell me how to do it ??
>

editconf -box

You can also adjust the positioning of the membrane within the box (for 
convenience in visualization or construction) with the -center option.

Then just fill the box with genbox/gmx solvate.  You may need to adjust 
vdwradii.dat to avoid spurious waters in the membrane core.

>   In my biological and other study I seen that  peptide forms the beta sheet
> structure and react with plasma membrane. Is it possible to show this
> effect with the DPPC lipid membrane or should I change in protocol and
> Lipid??
>

Your model should be of whatever experimental/physiological reality you wish to 
study.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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