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Viveca Lindahl

  • Email: vivecal@kth.se
  • Registered on: 10/09/2014
  • Last connection: 06/12/2018

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06/06/2018

11:31 AM GROMACS Feature #2547 (New): Add option of averaging and obtaining error bars for AWH PMFs
Statistical errors in the PMF calculated with AWH can be estimated by running multiple independent simulations. Curre...
11:20 AM GROMACS Task #2546 (New): Add more assertions to AWH code
The assertions in the AWH code are currently quite sparse. More should be added to secure future reorganization, e.g....

06/05/2018

11:03 PM GROMACS Bug #2489 (Fix uploaded): Handle mdp-option case "awh-nsamples-update = 0"

04/27/2018

05:26 PM GROMACS Bug #2494 (Closed): mdrun -noappend detects incorrect part
The command @for i in {0..3}; do gmx_debug mdrun -v -quiet -s topol.tpr -tableb table_b0.xvg -nsteps 10000 -cpi -noa...

04/26/2018

01:56 PM GROMACS Bug #2487: AWH covering detection delayed in certain cases
Berk Hess wrote:
> spacing=1/sqrt(betak)
> so the threshold is fixed at 0.4 and does not change with the number of ...
12:21 PM GROMACS Bug #2487: AWH covering detection delayed in certain cases
Berk Hess wrote:
> I don't see how the threshold depends on the number of points. It looks like the prefactor in the...
11:55 AM GROMACS Bug #2487: AWH covering detection delayed in certain cases
Berk Hess wrote:
> The covering frequency does not depend on descretization. The discretization is set by the force ...

04/25/2018

04:01 PM GROMACS Feature #2491 (New): Allow constant bias AWH simulations
Some users prefer to simulate in constant ensemble when applying a bias potential along a reaction coordinate. AWH ca...
02:34 PM GROMACS Bug #2489 (Closed): Handle mdp-option case "awh-nsamples-update = 0"
Setting "awh-nsamples-update = 0" is accepted by grompp but leads to a floating point exception because the variable ...
11:48 AM GROMACS Bug #2487 (Closed): AWH covering detection delayed in certain cases
For a Brownian dynamics system with a 2d reaction coordinate, the AWH detection of covering gets delayed because the ...

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