[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 19 15:13:12 CEST 2011

James Starlight wrote:
> Justin, hello!
> Today I've done 1ns npt equilibtation of my system
> this is the final result of this stage of simulation 
> http://www.sendspace.com/file/nw032q

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

> So I wounder to discuss some notes with imerged during the simulation
> 1- As you see some water molecules have moved into membrane during NPT 
> phase. Why it might occurs? I hope that during simulation hydrophobic 
> effect would exclude it from the membrane

If water is leaking into your membrane, you may have voids between the lipids 
indicating insufficient packing.  Also note that the hydrophobic effect does not 
mean that water cannot enter the membrane, it just means it should be a 
relatively infrequent event.  Most meaningful membrane protein simulations are 
tens or hundreds of nanoseconds long, first to equilibrate the membrane and 
surrounding water, and then to collect adequate data.

> 2- Also during the npt stage, the box size of the whole system in 
> Z-dimension was shrinked from 6.5 to 4.5 nm. Why this might occur?

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.

> 3- Finally on the finall MD stage I've obtained some notes form grompp
> NOTE 1 [file md.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
> What does it means?

Algorithmic nuances.  See the manual.

> NOTE 2 [file md.mdp]:
>   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
> I've found that exactly Nose-Hoover thermostat is more accurate for the 
> membrane proteins. But from that note it seems that this thermostat is 
> not supported by MD integrator, isnt it?

It is supported, but you cannot use multiple chains.  There is no problem here.



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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