[gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro
ramadavidgroup at gmail.com
Fri Oct 10 13:52:00 CEST 2014
Thank you a lot for immediate reply.
One more question:
Should I need to equilibriate the membrane after this one ??
With best wishes,
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.
>> concist 8 amino acid.I want to keep the two or four peptide just away
>> 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
>> 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
> Your model should be of whatever experimental/physiological reality you
> wish to study.
> 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
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