The GPU usage percentage of my Nvidia Quadro K3100M does not exceed 10% during running MD simulation of protein of 252 residue length using VMD/NAMD software. Any one can provide advice on how increase the GPU usage percentage to sped up the simulation process????
PME, bonded and non-bonded interaction are currently supported on GPU. So you can not go beyond that. You can add +idlepolls at the starting of a simulation. Recently NAMD team has introduced the NAMD3 alpha release, you can give it a try too. It is faster than NAMD-2.13.
Link - https://www.ks.uiuc.edu/Research/namd/benchmarks/
The problem appears to be because of your GPU itself. Quadro K3100M is a 2013 release and the NAMD version you are using might not have compatible code to utilize the GPU strength you are expecting. Better consult the NAMD version web page for GPU related details. Upgrading your NAMD version is also going to help if it supports the GPU. For older GPUs, they suggest you should stick to the older versions.
- Badges
- Science topic