Inconsistency between NAMD 2.11 and NAMD 2.12

From: Bryan Roessler (
Date: Tue Jan 31 2017 - 00:52:22 CST


I've been having problems with my free MD simulations in 2.12 and 2.12b1
that do not happen in 2.11. According to my logs the last known good build
that I was using was the 2015-10-29 nightly that did not have this problem.

I am using the CUDA enabled linux builds.

The problem is that immediately when I begin (or restart) a simulation
using one of the affected builds I see a large depression form in the
solvation box (it's not a PBC artifact, there is plenty of padding) and my
system temperature rises from ~310K to ~335K (and higher) and eventually my
simulation fails due to RATTLE constraints on some of the exterior
hydrogens of my protein.

I have tried restarting stable ~20ns simulations from the 2015-10-29 build
and they will usually fail within 100-1000 timesteps on 2.12 or 2.12b1. If
I restart the simulations in 2.11 they proceed perfectly. I thought that
there might be some compatibility issue between the binary files so I've
also exported the restart files as a PDB in VMD and reinitialized my
temperatures but this hasn't helped.

I thought that perhaps CUDA versioning was giving me problems so I made
sure to specify the correct LD_LIBRARY_PATH with the linked
included with NAMD.

I have also tried building NAMD but I will need to fire up a VM since there
are compatibility issues between GCC 5.3 and CUDA 8.0 and I don't want to
muck with my environment too much. I was hoping that maybe someone could
shed some light on this problem before I go that route.

The KISS in me says to just keep using 2.11 for the time being but I'd very
much like to utilize the GPU performance optimizations and I'm curious why
this happening. 2015-10-29 has decent performance too without the
associated problem so I will likely continue to use that version going
forward. I'd also be curious to find a ftp or some other site where I can
download older nightly builds so maybe I could narrow down when this
problem was introduced.


*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
* <>*
Knowledge that will change your world

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