From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 27 2012 - 00:28:03 CST
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.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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 <broomsday_at_gmail.com> wrote:
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
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.
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
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