[gmx-users] T-coupling of water and ion

[David van der Spoel]

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.
________________________________________________________________________
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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