Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5.
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). I have tried to sort this out myself by using the following settings: (1) change lincs_iter from 1 to 2. (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). (3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated. None of this seems to help. Actually Justin himself has helped me and found that with the following settings the conservation is considerably better === shift settings === vdwtype = shift coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.0 rvdw_switch = 0.8 Still there is a drift in the "conserved quantity" which seems a quite severe problem. Can anyone give some pointers on how to sort this out? Thanks -David
<<attachment: equil_nvt.png>>
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