Re: AW: Consistent temperature increase in CUDA runs

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Feb 28 2012 - 02:57:30 CST

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 havenít 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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.
>
> ~Aron
>
> On Mon, Feb 27, 2012 at 1:28 AM, Norman Geist <norman.geist_at_uni-greifswald.de> 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: 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:
> 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.
>
> ~Aron
>
>
> On Fri, Feb 24, 2012 at 1:51 AM, Norman Geist <norman.geist_at_uni-greifswald.de> 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
>

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