[gmx-users] Re: Wheter the drift velocity has been removed from calculating the temperature?

[David van der Spoel]

Hu Zhongqiao wrote:
> 
> 
>> > I wonder if the drift velocity has been removed from calculating the
> 
>> > temperature for a non-equilibrium MD in which a directional movement for
> 
>> > a group exists due to external force applied.
> 
>  
> 
>>  Yes it is. Please check the source code in src/mdlib/update.c
> 
>  
> 
> Thanks, David.
> 
>  
> 
> Then how can I get the temperature profile as the function of time? In 
> my simulation, the first group as mobile phase is driven by external 
> force, the second is fixed as stationary phase. I have turned off the 
> COM removal. Both the log file and g_energy give temperatures (about 320 
> K) obviously higher than one (300 K) I set. I guess it is due to the 
> drift velocity. Is there a good way to get the temperature profile which 
> is corrected by removing drift velocity?
> 
>  
> 
> Zhongqiao
> 

If you have saved velocities you can use g_traj to extract both group 
velocities
and temperatures, but the T in this case are not corrected for 
constraints or group velocities. Please do also check the source code.


-- 
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