[gmx-users] Fwd: "Solved the issue on annealing - so to speak "
paul buscemi
pbuscemi at q.com
Fri Jul 27 22:42:47 CEST 2018
>
> To work around the single point annealing I had to add three single groups. Here I tried to use the first group as the ramp and the second two as constant
>
>
> It turns out the number of groups the online definition gives and that mdp wants is not the number of temperature groups , but the number of molecular groups. see the grompp output below.
>
> isolating ramps for individual molecule groups is a great advantage, but the description in the mdp/options page is indeed confusing.
>
> ====== work around with three single temperature groups ===========
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing = single single single
>
> ; Number of time points to use for specifying annealing in each group
> annealing-npoints = 2 2 2
>
> ; List of times at the annealing points for each group
> annealing_time = 0 500 0 10 0 10
>
> ; Temp. at each annealing point, for each group.
> annealing_temp = 100 320 320 320 320 320
>
> ============ grompp output ==========
>
> Simulated annealing for group Z8G5: Single, 2 timepoints
> Time (ps) Temperature (K)
> 0.0 100.0
> 500.0- 320.0
> Simulated annealing for group NIGR: Single, 2 timepoints
> Time (ps) Temperature (K)
> 0.0 320.0
> 10.0- 320.0
> Simulated annealing for group ISOP: Single, 2 timepoints
> Time (ps) Temperature (K)
> 0.0 320.0
> 10.0- 320.0
> Number of degrees of freedom in T-Coupling group Z8G5 is 94389.77
> Number of degrees of freedom in T-Coupling group NIGR is 16199.62
> Number of degrees of freedom in T-Coupling group ISOP is 15999.62
>
>
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