Dear all<div>I have been following Justin Lemkul's tutorial for the lysozyme simulations</div><div><a href="http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html">http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html</a></div>
<div>I am using Gromacs 4.5.5. </div><div><br></div><div>My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling thermostat. In step 6 of the tutorial an NVT equilibration is run using tcoupl = V-rescale. The temperature equilibrates quite rapidly as shown in Justin's webpage. Essentially, T fluctuates around its equilibrium value after ~ 2 ps. However looking at the "conserved energy" I find that there is a drift that does not seem to plateau even by the end of the 100 ps run (see attachment).</div>
<div><br></div><div><font style="background-color:rgb(255,255,255)">I have tried to sort this out myself by using the following settings:</font></div><div><div style="font-family:arial,sans-serif;font-size:13px"><font style="background-color:rgb(255,255,255)">(1) change lincs_iter from 1 to 2.</font></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font style="background-color:rgb(255,255,255)">(2) change from PME to PME-Switch, which for NVE Gromacs recommends as more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4).</font></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font style="background-color:rgb(255,255,255)">(3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated.</font></div></div><div style="font-family:arial,sans-serif;font-size:13px">
<font style="background-color:rgb(255,255,255)">None of this seems to help.</font></div><div style="font-family:arial,sans-serif;font-size:13px"><font style="background-color:rgb(255,255,255)"><br></font></div><div style="font-family:arial,sans-serif;font-size:13px">
<font style="background-color:rgb(255,255,255)">Actually Justin himself has helped me and found that with the following settings the conservation is considerably better</font></div><div><font style="background-color:rgb(255,255,255)" face="arial, sans-serif"><div>
=== shift settings ===</div><div>vdwtype = shift</div><div>coulombtype = PME</div><div>rlist = 1.4</div><div>rcoulomb = 1.4</div><div>rvdw = 1.0</div><div>rvdw_switch = 0.8</div><div>Still there is a drift in the "conserved quantity" which seems a quite severe problem.</div>
<div><br></div><div>Can anyone give some pointers on how to sort this out?</div><div>Thanks</div><div><br></div><div><br>-David</div></font></div>