[gmx-users] temperature too low

[Anton Feenstra]

w.j.schravendijk at students.pharm.uu.nl wrote:
>  
> On Tue, 26 Feb 2002, David van der Spoel wrote:
> 
> > Since your temperature is exactly two/thirds of what it should be, it
> > could be that you have a problem with the number of degrees of freedom.
> 
> It seems that the simulation has run correctly, but that g_traj generates
> the wrong output. Is there any way I could fix this? Are there other
> g_** programs that are vulnerable for the value of the degrees of freedom?
> 
> BTW: (I've checked cut-off as well as PME and gen forcefield, it all
> resulted in the 2/3 temperature output from g_traj)

 From 'g_traj -h':
``
Option -ot plots the temperature of each group, provided velocities are present
in the trajectory file. No corrections are made for constrained degrees of
freedom! This implies -com.
''

g_traj was never intended to check the system temperature, but it was
a simple option to implement. It assumes nrdf = natoms * 3, which is
wrong as soon as there are constraints in the system (as the manpage
says). Correct temperatures are stored in the energy (.edr) file and
can/should be extracted using g_energy. I realize this is not really
intuitive, so this deserves some thought from us (the developers)...

But, I could also have said: RTFM... ;-)
-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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