[gmx-users] (no subject)

[Anton Feenstra]

Nguyen Hoang Phuong wrote:
> 
> Dear Gromacs Users,
> 
> I have simulated the peptide in H2O. The simulation has been done
> as the following:
> 
> 1)Energy minimization with fixed peptide
> 
> 2)simulating for 5ps with fixed peptide
> 
> dt    = 0.002
> tau_p = 0.05
> tau_t = 0.01
> 
> 3)simulating for next 5ps without position constraining of peptide
> 
> dt    = 0.002
> tau_p = 0.1
> tau_t = 0.01
> 
> 4)Long run:
> 
> if( tau_t = 0.1)  -->  I get the temperature shifted about +10K
> if( tau_t = 0.01) --> I get the right temperature
> 
> (tau_p = 0.1, dt =0.002)

I don't know if this explains your temperature shift, but in general
it is discouraged to use temperature and pressure coupling times of
the same value, because that can cause unwanted feed-back oscillations
between both coupling mechanisms.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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