[gmx-users] Simulation of membrane protein

[James Starlight]

In some papers I found Gromacs graphs showed indirectly measurements of the
time evolution of the Area per lipid value. What gromac's program could be
used for it for cheacking the above value during simulation runs ?

JAmes

2011/10/29 James Starlight <jmsstarlight at gmail.com>

> It's appeared new question about G_membed
>
> Does anobody used this algorithm for insertion of their proteins ?
> In particular I wounder to know how I can to find optimal parameters (
> different scaling factors like in the below command) for insertion in my
> system( single alpha helix in DMPC bilayer system) and how I can measure
> area per lipid in the output system?
>
>    g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
> -zinit 1.1 -zend 1.0 -nz 100
>
>
> James
>
>
> 2011/10/25 Justin A. Lemkul <jalemkul at vt.edu>
>
>>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> I've found the same task of MSU's students :) They simulate membrane
>>> formation without NPT stage ( after NVT they run production MD). From they
>>> reports I've found that simplest membrane system could be formed within
>>> 10-30 Ns.  But what about try to make such simulation in vacuum at first
>>> without any water ? Might the bilayer been formed in such conditions?
>>>
>>> Finally I have small question about pereodic boundaries of such bilayer
>>> system.
>>>
>>> E.g I've done simplest system with water consisted of 8 lipid molecules
>>> + some water.
>>> This is the representation of the system http://i1209.photobucket.com/**
>>> albums/cc394/own11/lipids8.png<http://i1209.photobucket.com/albums/cc394/own11/lipids8.png>
>>> I want to simulate bilayer formation as well as concomitant hydrophobic
>>> effect ( removing all water from formed bilayer)
>>> Does the PBC presented in that example ( 2.64196   2.64196   6.85002 for
>>> 8 lipids) are enought for such lipid movement? It seems that more free
>>> space aree needed for overal turn of lipid molecules. How I can calculate
>>> exactly  PBC value required for my system ?
>>>
>>>
>> I agree that your system has insufficient space for any real movement
>> without violating the minimum image convention.  Your system must have
>> adequate room for any lipid to rotate in any direction, and be of
>> sufficient size to accommodate a formed membrane, which will have
>> dimensions dictated by the APL for the chosen lipid (and of course, the
>> force field's ability to produce that value).
>>
>>
>> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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