Justin, hello!<br><br><br><br>Today I've done 1ns npt equilibtation of my system<br>this is the final result of this stage of simulation <a href="http://www.sendspace.com/file/nw032q">http://www.sendspace.com/file/nw032q</a><br>
<br>So I wounder to discuss some notes with imerged during the simulation<br><br>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<br>
<br>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? <br><br>3- Finally on the finall MD stage I've obtained some notes form grompp<br>
<br>NOTE 1 [file md.mdp]:<br> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting<br> nstcomm to nstcalcenergy<br><br>What does it means?<br><br>NOTE 2 [file md.mdp]:<br> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1<br>
<br>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?<br><br><br>James<br>