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 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? James
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