AW: AW: Consistent temperature increase in CUDA runs

From: Norman Geist (
Date: Wed Feb 29 2012 - 00:17:26 CST



Thank you all very much for your answers. I've done some comparison
simulations of NAMD with cpu and a precompiled and self compiled NAMD CUDA.
The temperature raise is present in all of them, the funny thing is that the
raise is the highest on cpu, what might be fluke. You are likely right with
the multible timestepping as we use fullelectfrequency 4 for performance
reason on the GPUs. I will try with setting to 1 and look what happens. I
could also try zeromomentum although the system doesn't seem to drift. If
all that doesn't help, I will maybe use temperature rescaling with a large
frequency of about 1ns to hold the systems temperature or what do you think?


Thank you


Norman Geist.


Von: [] Im Auftrag
von Vlad Cojocaru
Gesendet: Dienstag, 28. Februar 2012 10:25
An: JC Gumbart
Betreff: Re: AW: namd-l: Consistent temperature increase in CUDA runs


We've done some tests and multiple time stepping does not conserve energy.


On 02/28/2012 09:57 AM, JC Gumbart wrote:

I'm not sure that multiple-time stepping conserves energy (someone correct
me if they know otherwise!). Try running with a uniform time step to see if
you get different results.



On Feb 28, 2012, at 12:19 AM, Norman Geist wrote:

Hi Aron,


thank you for investigation. What you see might be unfortunately, too.


The problem I see, arises also in CPU runs as I now think. It was harder to
observe for me as we haven't done long simulations on CPU with namd. In
temperature controlled runs, everything is fine with the temperature. Then
we do a free simulation without any controlles afterwards, were the
temperature keeps consistently rising. Strange! I got to test a little.
Maybe increasing pairlistdist and switchdist helps but I already have


cutoff 10

switchdist 7

pairlistdist 14


What else might affect energy conservation?


Thanks you


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Montag, 27. Februar 2012 15:32
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Consistent temperature increase in CUDA runs


Hi Norman,

Yeah I had temperature controlled for the whole run.

In doing a more thorough examination of the kinetic energies though, I've
come across something very odd. In my case I have ~2000 atoms from a medium
sized protein, and the rest (98,000) is solvent. I have rigid water on, but
have left the protein hydrogens non-rigid, and am using a 1fs timestep, with
langevin Hydrogen coupling off. What I see is that the kinetic energy
distribution of the non-rigid atoms matches my desired temperature, but when
I break it down into sub-systems, I find that the temperature of all the
protein atoms comes out ~20-25 K higher than the solvent!!

That is a pretty extreme difference. I figured maybe it was because of I
decoupled the bath from the hydrogens, so I ran an extra 2 ns with it
coupled but saw no change in the crazy distribution of temperature. I'm
doing some more testing, and although it doesn't seem to relate entirely to
what you are seeing, it seems like a big problem. I'm also not certain if
it is GPU specific at this point.


On Mon, Feb 27, 2012 at 1:28 AM, Norman Geist
<> wrote:

Hi Aron,


thank you for your interest. My system sizes are mostly about a million
atoms, but the problem also occur in smaller systems. Have you measured out
this data you gave from a temperature controlled run, or was the temperature
free? I also heated up my system with the langevin and let in run
uncontrolled afterwards, while langevin is active, temperature is fine, but
when turning off, a slow increase of temperature occurs. The system is also
on 1 atm pressure.


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Samstag, 25. Februar 2012 02:53
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Consistent temperature increase in CUDA runs


Having looked around a little more, I'm wondering if hydrogen coupling might
have anything to do with it. I've got Langevinhydrogen set to off, which I
thought was the correct thing to do when using rigid waters (like TIP3P)
even if the other hydrogen bonds in the system are not rigid. Maybe I'm way
off base here.

On Fri, Feb 24, 2012 at 3:49 PM, Aron Broom <> wrote:

Hi Norman,

I've been running simulations in NAMD using AMBERFF03 and GLYCAM06 on GPUs
(M2070 mostly). I dragged out some old files from a 60ns run, and checked
the temperature at 10ns with that at 60ns by directly computing it from the
velocity files that were written at the end of each 10ns segment. I was
using Langevin dynamics set to be 300K, I get 297K at 10ns, and 296K at
60ns. So I'm not seeing what you see.

For reference, I was using 1fs, 2fs, 4fs multi-time-stepping with only
waters being rigid (SETTLE). The system size was ~101,000 atoms. I was
also using pressure control at 1 atm.

Now, this being said, every 10ns the system was restarted, but the
velocities were not rescaled, they were taken from the restart velocity file
along with the coordinates and extended system information, and I think the
random seed was even the same at all restarts (which was probably stupid,
but not relevant to this discussion), so I imagine this should have been the
same as just running one long 60ns simulation.

Is your system considerably smaller than mine? Perhaps the error creeps up
more slowly with more particles.



On Fri, Feb 24, 2012 at 1:51 AM, Norman Geist
<> wrote:

Hi experts,


we got a little issue here. We use NAMD on CPU and GPU with the amber FF.
The systems run fine on CPU, but come with a consistent increase in
temperature when running on GPUs. Is that a known problem. What to do about
it. The rise is ca. 25K over 40 ns, so long simulations cannot be done
without many rescales.


Any ideas?


PS: The system does not contain fixed atoms.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]

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