From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Feb 28 2012 - 03:24:30 CST
We've done some tests and multiple time stepping does not conserve energy.
Best,
Vlad
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:*owner-namd-l_at_ks.uiuc.edu
>> <mailto:owner-namd-l_at_ks.uiuc.edu>[mailto:owner-namd-l_at_ks.uiuc.edu]*I**m
>> 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
>> <mailto: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>[mailto: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
>> <mailto: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
>> <mailto: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
>>
>
-- 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]mpi-muenster.mpg.de
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