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

[rama david]

Dear Justin,
 Thank you  a lot for immediate reply.
 One more question:
   Should I need to equilibriate the membrane after this one  ??

With best wishes,
Rama David

On Fri, Oct 10, 2014 at 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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