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When estimating a restraint free energy by changing the force constant (section 6.5.3 in the user guide), dA/dLambda is accumulated and printed in the log file (without any measures of dispersion).
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Hello, I have encountered some problems when I calculate phonon free energy with dynaphopy, hope to get your help.
1. The harmonic phonon free energy calculated by dynaphopy and phonopy are very di…
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I tried the example of absolute binding energy calculation of p-Xylene to T4-Lysozyme in explicit solvent with the yaml file provided in the website withot any changes. My results show free energy of …
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The memory requirements of TensErLEED (especially the refcalc) can become quite limiting when tackling large unit cell systems. @LutzHammer reported needing about 25 GB of memory per energy step in th…
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Hi,
Is the *.properties.out the best place to parse the final energy (energy containing the CPCMX correction)? I understand that the energy printed in this file will always contain the CPCMX term, …
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When we refactor the relative alchemical factory to move it to `openmmtools`, we should consider allowing multiple alchemical regions to enable A->B and B->A transformations to happen with the same si…
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Dear OpenMM community,
We (the Riniker lab @rinikerlab and the Hünenberger lab @csms-ethz at ETH Zurich) have developed a shifted reaction-field (RF) correction (https://doi.org/10.1039/D0CP03835K…
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It probably should be; it's supported in the biggest simulation engines, has valid scientific basis, and sees use in force fields elsewhere.
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The file link:http://rashmikumari.github.io/g_mmpbsa/tutorial.tar.gz
~/tutorials/pbsa.mdp
Line 90, sasaconst = 3.84982
It should be 'sasaconst = 3.84928'
as you have refered in the article,
Wang,…
ghost updated
6 years ago
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### Description
The function hoomd.update.RemoveDrift() currently updates the position of all particles in the simulation. I would like to be able to pass a subset of particles so that the center-of-…