GaMD is slower on GPU compared to cMD

From: Venkatareddy Dadireddy (
Date: Mon Sep 06 2021 - 11:15:00 CDT


I am new to NAMD and want to use GaMD module in NAMD v3.0 alpha 9.
I am following the protocol:;!!DZ3fjg!uR1u8UbK1TFiJzQDS6AOXJL5n-T_Ix3kl2O2GXTKg3JCKqO2SpouKhK1oiwSvSAUeGI_SzA$
I am using some tutorial test file (pdb) to get hands on GaMD/NAMD.
When I run conventional MD (cMD) on my test system, it runs quite faster
(160ns/day) on single GPU. But when I use the same system for GaMD,
it takes >3days with the following preparatory steps.

accelMDGcMDPrepSteps 200000
accelMDGcMDSteps 1000000
accelMDGEquiPrepSteps 200000
accelMDGEquiSteps 25000000
timestep 2.0 # fs

What I found is that 'CUDASOAintegrate on' accelerates the simulations
but in case of GaMD equilibration and production steps the
'CUDASOAintegrate on' is not supported.
In case of cMD, >90% GPU is used but in case of GaMD , only 13% of
GPU is utilized.
Please help me solving this problem.

Thank you,

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