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Miroslav Suruzhon

  • Registered on: 01/30/2019
  • Last connection: 02/18/2019

Issues

Activity

02/13/2019

10:12 AM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> I found the mass Delta H double counting issue and uploaded a fix to 2019. We should backport thi...

02/12/2019

11:46 AM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> I see the exponential issue now. The mass and constraint terms do not affect the Boltzmann distri...
10:27 AM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> But how do you compute the exponential free-energy difference? gmx energy can not compute the mas...

02/11/2019

02:58 PM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> The exponential is a crude approximation, so I'm not surprised that is far off.
> But the (M)BAR...
11:24 AM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> > Okay, that makes sense. The total energy should then contain all terms we would want for a corr...

02/08/2019

12:20 PM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> The constraint contribution can not be obtained from the potential, there is a kinetic contributi...
11:20 AM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> I don't understand what you mean with "potential energies". The Coulomb+bonded leg has both mass ...

02/07/2019

03:53 PM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> Your lambda 0 tpr gives me identical dhdl.xvg files with 2018.4 and 2019, as I would expect.
> W...
12:52 PM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> The tprs you attached perturb both charges and masses. So my hypothesis is still that the Coulomb...
12:16 PM GROMACS Bug #2849: Free energy discrepancies between GROMACS versions
Berk Hess wrote:
> So issue I am aware of:
> <= 2018.3: mass and constraint contributions missing in Delta H (dH/dl...

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