[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Wed Oct 19 15:32:50 CEST 2011


> As I said before, I cannot obtain files from this site.

Could you provide me with the fileshare server wich you have access? I cant
uploat files to that mail list indirectly due to the limitation of the size
for attached files

> If water is leaking into your membrane, you may have voids between the
> lipids indicating insufficient packing.   I'm willing to bet that there are
> some voids somewhere in the simulation box at the outset of the simulation,
> likely due to the use of an increased vdW radius for carbon.  The solvent
> will fill in the voids over time and the box will change accordingly.

It's intresting that water leaking was detected after NPT equilibration
exactly. ( after solvating and NVT there are no water molecles inside the
membrane ) .  Also I've checked how the temperature, pressure and XYZ
bondaries of the box have being stabilized and there were not any deviation
from the results presented in the tutorial.

Also I've tried to prepare same system with the G_membed. Firstly there were
removed 4 lipids in comparison to perl program wich removed only  2 lipids.
Finally a fter minimisation of that system there already has been some water
inside the membrane. By the way I'll try to equilibrate this system and
examine results.

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