[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 19 15:50:38 CEST 2011

James Starlight wrote:
> Justin,
>     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 

I don't need the files.  I'm just trying to save you time.  If I want to see a 
coordinate file, I'll ask for it to be sent to me directly.  I have seen no such 
need yet.

>     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.

Application of pressure causes the box to change.  The water won't leak in 
during NVT because the components of the system are trying to keep the box full 
since its dimensions are invariant.

> 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.

Such leakage is typical during equilibration, as I've said.  You should not be 
alarmed by this result.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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