NAMD related theoretical questions

From: Kostas Malavazos (
Date: Wed Jul 20 2016 - 12:33:11 CDT

Hello everyone,

I have finished my work on implementing the long-ranged non-bonded forces
on FPGA, using the CUDA code from NAMD 2.10. Nevertheless I need some
instructions about this code, as the NAMD 2.10 lacks documentation. The
instructions I need, include the theoretical background of the CUDA code
(e.g. functionality of loop blocki, loop blockj, input data, output data,
how the atoms are distributed to the patches etc.). I am a student in the
Technical University of Crete, Electrical and Computer engineering
department, so chemistry and biology are not my areas of expertise. But in
my diploma thesis I have to explain, the functionality of the code,

The code from the CUDA file that I used is from
"ComputeNonBondedCUDAKernelBase.h" and the benchmark of ApoA1.

*Can anyone help me?*
Thanks in advance for your time,

Konstantinos Malavazos, undergraduate student
Microprocessor & Hardware Lab
Electrical and Computer Engineering
Technical University of Crete

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