On Tue, 2012-05-15 at 09:17 +0100, David de Sancho wrote: > 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.
Compiled in double or single precision ? If the latter one is the case, perhaps numerical errors are the reason for the large energy drift. /Flo > > > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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