-
Hi,
While using the enkephalin example which is based on the MM3pro ff, I've experienced that the numerical and analytical Hessian elements can differ much. For instance:
Comparison of Analytical …
-
Contact: Chao Peng / 504449847@qq.com
PLS-DA，和OPLS-DA，微生物组学和代谢组学都可以用到
-
I am working with a self assebmled system that consists of four ligands bridged together with two Pd(II) ions to form a nano-capsule. Both the ligands and the metals are parameterised with the ffld se…
-
# Description
Currently, `Impact` class is not tested. We should design some tests to check it out.
-
Hi All,
I was wondering if a features such as Schrodinger's 'getBondedEnergyComponents' or 'getNBEnergyForTwoAtomLists' in OPLS3 exists as a part of the OpenMM API. These functions evaluate the energ…
-
After transferring data from the spreadsheet to the wiki, then exporting from the wiki, do some sanity checks that the data still match the original spreadsheet. Doesn't have to be exhaustive, but, fo…
-
As discussed in the paper, the octanol model used in MDPOW underwent a phase transition to a dense solid phase during the simulation at 273 K.
We should update with the parameters from Zangi R (2018)…
-
In the current foyer xml implementation, connections can be defined either by `name` or `class` (example: https://github.com/mosdef-hub/foyer/blob/master/foyer/forcefields/xml/oplsaa.xml). This is ve…
-
Tagging @rafwiewiora here. This issue will discuss our conversion and validation of all forcefields distributed with AmberTools15.
@swails: Do you already have some validation scripts to use ParmEd …
-
Hi all, I was wondering if there might be a simple way to mask particular atoms and molecules when calculating the system energy -- this would be useful for getting the energy changes for monte carlo …