[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Fri Oct 21 10:48:27 CEST 2011

Justin, thanks again for the information

 Different force fields require different settings, most notably cutoffs.
> Understanding the intrinsics of the chosen force field is a prerequisite for
> using it.  Again, time spent in the literature here is more valuable than me
> spitting out settings that you should use.  You'll learn far more by
> discovering it yourself.
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?


> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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