[gmx-users] Cosine bending potential

Hi, What is the function no. (funct) for the functional form of the bending potential U_bend = k_theta*(cos theta - cos theta_0)^2 ? Thanks and Regards, Arnab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi Szilárd, Thanks for your tips. It turned out that between installing AMDGPU-PRO, then AMD APP SDK, the link to libopencl.so became broken. Following your suggestions (if I interpreted them correctly), I linked against the copy installed by AMDGPU-PRO. That resolved the error and I was

Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi Gregory, First of all, I'd strongly recommend you to start with the 2016 release, 2016.1 has been out for some time. This will be more robust and has a lot of performance improvement too especially on AMD (see http://manual.gromacs.org/documentation/2016/ReleaseNotes/). Regarding the link

Re: [gmx-users] PMF decompostion

Thanks David and Christopher for your responses. I do not understand why vdW and Q are not meaningful contributors of PMF as a biasing method, as I think one can loop over the trajectory of all the biasing method either from US or Metadynamics and recompute the force separating vdW and

Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi Milan and Szilárd, Many thanks for your comments. So I installed Ubuntu 16.04, installed the AMDGPU-PRO driver, installed the AMD APP SDK. Then I attempted to install GROMACS 5.1.4 as follows: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON

[gmx-users] Ligand-protein free binding energy is become positive

I’m using MM-PBSA on gromacs to calculate free binding energy of some ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and to setup a rational threshold for evaluating the results, the co-crystal ligand was considered as the reference ligand. Results showed that free binding

[gmx-users] adding lcudart C++ flag + -cudart=shared NVCC flag to compile option

Hello, how can i add those two flags to their respective compiler? i want to force Gromacs to compile using those options but im not quite used to messing with various CMake option. Thank you -- Gromacs Users mailing list * Please search the archive at