[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Wed Oct 19 08:40:46 CEST 2011

Justin, hello!

Today I've done 1ns npt equilibtation of my system
this is the final result of this stage of simulation

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

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?

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?

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?

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