A incorrect initialization of a variable in TINKER 6.0.04 leads to the use of non-periodic boundary conditions for the AMOEBA plugin vdw force for calculations employing PME. The initialization was corrected in TINKER 6.0.05 If you are using TINKER 6.0.04, the fix is to edit unitcell.f and change 'n...

Hi Akila,

Try adding one of the following lines to the TINKER key file:

integrator VERLET

or

integrator STOCHASTIC

Mark

<t>Hi Jaehyun,<br/> <br/> I would first try removing the free energy plugin from the build; the error messages are coming from attempts to link to methods included in the free energy plugin libs. When you run Cmake, set the values of the variables names OPENMM_BUILD_FREE_ENERGY_PLUGIN and OPENMM_BUI...

<t>Hi Francesco,<br/> <br/> The code for the nonpolar term used for implicit solvent calculations is carried out for the Reference platform in CpuImplicitSolvent::computeAceNonPolarForce() in the file platforms/reference/src/gbsa/CpuImplicitSolvent.cpp and for the Cuda platform in kReduceObcGbsaBorn...

<r><br/> Hi,<br/> <br/> If you get a message box stating 'Reverting to Reference Platform' even though you have Cuda installed then the problem might be due to Zephyr being unable to find the required Cuda dlls.<br/> The Cuda libs for the current version of Zephyr (2.0.2) were compiled against Cuda ...

The Cuda files can be downloaded from http://www.stanford.edu/~friedrim/cudart32_31_9.dll and http://www.stanford.edu/~friedrim/cufft32_31_9.dll

<t>Hi Brian,<br/> <br/> The Cuda libs for the current version of Zephyr were compiled against Cuda 3.1. If you have a different version of Cuda installed, the program will not find the required runtime lib ('cudart32_31_9.dll') in the Cuda 'bin' directory. For example, if you have Cuda 3.2 installed...

Hi Jeff,

Zephyr/OpenMM does not currently support the GROMOS96 force field. If you want to get the speedup of OpenMM through Zephyr, you would have to generate a tpr for one of the Amber force fields.

Mark

<t>Hi Siddharth,<br/> <br/> My understanding is that the OBC parameters (radii in the params.agb file and the hardwired scale factors in Gromacs-OpenMM) are based on Amber force-field parameterizations. We have radii for protein atom types for Amber94 and Amber99 -- I can pass these on if it would h...

The return value -2 in

exception: Error initializing context: clCreateContextFromType (-2)

corresponds to CL_DEVICE_NOT_AVAILABLE