[gmx-developers] [gmx-users] Wrong Nose-Hoover integrator
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 7 13:52:16 CET 2007
Michel Cuendet wrote:
> To maybe conclude this old thread about calculating the temperature
> within a leap-frog scheme, a little paper just came out :-)
Berk implemented this in GROMACS a few years ago.
/* Calculate the full step Ekin as the average of the half steps */
for(j=0; (j<DIM); j++)
for(m=0; (m<DIM); m++)
0.5*(tcstat->ekinh[j][m] + tcstat->ekinh_old[j][m]);
> Berk Hess wrote:
>> If the (say correct) half step temperature of 300 K gives a full step
>> of 297.8 K, this means that the actual temperature of all water
>> done with Gromacs is 2.2 K too high as we couple the full step
>> to 300 K. It is even worse for my 4 fs water runs, which are 9 K too
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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