[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Fri Nov 11 20:07:56 CET 2011


The system was compact after inserting protein into bilayer (I've obtain
Area per lipid in accordanc with experimental reference) and futher
minimization (only some llipid tails on the border of the system were
distorded alittle)
But after  nvt simulation this discrepancy occured :)

I've used pbc size like in the KALP simulation because I have bilayer  (
128 lipids) and the protein (38 a.a) of the same size.
My box vectors were 6.500 6.500 6.500

Do you think that I should use smaller pbc? How I could define pbc on the
right size for my purely bilayer system?

I've used

trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact
at the preequilibrated bilayer and than done anything in accordance to
the KALP tutorial


2011/11/11 Justin A. Lemkul <jalemkul at vt.edu>

> How large of a void exists between your lipids and water prior to starting
> the simulation?  I'm almost certain that you built the unit cell
> incorrectly - there should never be that much free space.
>> By the way I'ts intresting that Gmembed has removed 6 lipids in
>> comparison to the inflateglo ( althought I've done all things in accordance
>> to the KALP tutorial because my protein is the same).
> Different algorithms, different results.  Nothing odd about that to me.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
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> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
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