[gmx-users] Simulation of membrane protein

[James Starlight]

Justin,

Could you tell me if I want to simulate self-organization of the pure lipid
bilayer starting from the initial random placed molecules in water. Does
this simulation need in pre-md NVT and NPT equilibration? What the average
time for NPT? I think that If this stage should occur it must be consist of
long ( tens of NS ) preequilibration.



James

2011/10/21 Justin A. Lemkul <jalemkul at vt.edu>

>
>
>
>  You'll learn far more by discovering it yourself.
>>
>
> I stand by this statement.  Perhaps some kind person with sufficient time
> on their hands will do your literature searching for you, but I do not,
> sorry.  The information you need is out there.  Start with the primary
> citation for whatever force field you want and search databases for citing
> articles or check out the references therein.  Even Google can pull up very
> useful results within seconds, provided you've given sufficiently specific
> keywords.
>
> -Justin
>
>
>>
>> That's why at the present moment I'm examining different force fields and
>> their implementation to the different systems. Could you recomend me some
>> survey arcticle when I could find something usefull for this ?  In
>> particular I wounder to know about parametrisation for the membrane systems?
>> Previosly I've found that charmm ff is ,ost accurasy in the case of such
>> examination but I've not been able to rapametrise my bilayers via this ff
>> yet ;x
>> On other hand I have not difficulties with GROMOS ff for different systems
>> ( e.g I've obtained very stabile systems durins some ns of simulations but I
>> dont know about accuracy of the parametrisation of this ff in the case of
>> membrane system for example .
>>
>> Finally I'm looking for tutorial for simulation of the pure lipids. E.g I
>> want to simulate of different physical events on my membrane ( e.g I want to
>> overkill my membrane by hyperpolarisation or other electrostatic effects
>> emerged on the different steps of my simulation ) Could you also recomend me
>> methodical literature for this styding?
>>
>>
>>
>> James
>>
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
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> --
> ==============================**==========
>
> 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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