[gmx-users] Fwd: Regarding correct way to calculate diffusion constant

-- Forwarded message -- From: Apramita Chand Date: Fri, Aug 26, 2016 at 6:56 PM Subject: Regarding correct way to calculate diffusion constant To: gmx-us...@gromacs.org Dear All, I want to calculate the diffusion constant of urea in my system. I used

[gmx-users] Tabulation table error

Dear gromacs user, I am trying to learn how to use tabulation table because I need a mix of Lennard Jones and Buckingham interaction. The tabulated simulation ran for a few ps before crashing with this error: A list of missing interactions: Angle of730 missing 1

[gmx-users] Improving GPU performance on Bridges HPC cluster

Hello Gromacs users, Our group has begun running simulations on the XSEDE resource, Bridges, and we are trying to maximize our performance on the GPU nodes. The nodes are configured so that there are two Tesla K80 accelerators each consisting of 2 GK210 GPUs. Additionally, there are two CPU's on

Re: [gmx-users] Improving GPU performance on Bridges HPC cluster

Hi, Have you checked onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full, especially Fig 8? A few things I noticed while scrolling through briefly: - You-re not pinning threads in mdrun; (the excessive CPU-GPU balancing with quarter vs full node runs is suspicious)/ - Typically multiple ranks per