[gmx-users] T-coupling of water and ion
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 1 09:09:59 CEST 2005
On Wed, 2005-06-01 at 09:58 +0800, Jian Zou wrote:
> Hi Anton,
> Thanks for your comments.
> Anton Feenstra wrote:
> > And which ref_t did you use during PR-MD?
> 400K, too.
> > Your *whole* system is (far) below the 400K ref_t. I can't see how your
> > mdp file could have produced these results. Are you sure these are the
> > settings you used? Perhaps you can check your .tpr file or md.log (or
> > md0.log)?
> I use g_energy to generate the temperature again, using
> > g_energy -f md_ener.edr -o T-ener.xvg
> and choose
> Temperature, T-RNA, T-SOL, T-Na
> the results are as follows
> # time Temperature T-RNA T-SOL T-Na
> 0.000000 394.552277 396.710052 394.425232 261.817810
> 2.000000 401.028137 390.325897 401.582977 243.876129
> 4.000000 402.511139 411.360046 402.510193 337.482910
> 6.000000 398.780670 425.899078 398.483795 407.033661
> This time, the above result is likely to be what I want.
> I don't know why the g_energy results from ener.edr is so different from the
> g_traj results from the trr file.
> how to understand the difference?
This is because g_traj does not know about constraints. If you get water
temperature from g_traj after simulating with shake/lincs/settle you
have to multiply it by 1.5, because g_traj assumes three degrees of
freedom per atom while there are onyl two.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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