[gmx-users] energy drift - comparison of double and single precision

[XAvier Periole]

Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?

 Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. 

XAvier. 

> On Oct 12, 2013, at 0:50, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
> 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than
> that. I bet the rest of the lysozyme model physics is not accurate to less
> than 1% ;-) There are some comparative numbers at
> http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather
> different but they share the use of SETTLE.
> 
> Note that using md-vv guarantees the 2007 paper is inapplicable, because
> GROMACS did not have a velocity Verlet integrator back then. Sharing the
> .log files might be informative.
> 
> Mark
> 
> 
> On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot <
> guillaume.chevrot at gmail.com> wrote:
> 
>> Hi,
>> 
>> sorry for my last post! I re-write my e-mail (with some additional
>> information) and I provide the links to my files ;-)
>> 
>> I compared the total energy of 2 simulations:
>> lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3
>> lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3
>> 
>> ... and what I found was quite ... disturbing (see the plots of the total
>> energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a
>> constant
>> drift in energy in the case of the single precision simulation.
>> 
>> Did I do something wrong*? Any remarks are welcomed! Here is the link to
>> the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you
>> can check what mdp options I used.
>> 
>> My second question is: if I did not do something wrong, what are the
>> consequences on the simulation? Can I trust the results of single precision
>> simulations?
>> 
>> Regards,
>> 
>> Guillaume
>> 
>> *PS: I am not the only one encountering this behavior. In the literature,
>> this problem has already been mentioned:
>> http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1
>> 
>> 
>> 
>> 
>> 2013/10/11 Mark Abraham <mark.j.abraham at gmail.com>
>> 
>>> On Oct 11, 2013 7:59 PM, "Guillaume Chevrot" <
>> guillaume.chevrot at gmail.com>
>>> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> I recently compared the total energy of 2 simulations:
>>>> lysozyme in water / NVE ensemble / single precision
>>>> lysozyme in water / NVE ensemble / double precision
>>>> 
>>>> ... and what I found was quite ... disturbing (see the attached figure
>> -
>>>> plots of the total energy). I observe a constant drift in energy in the
>>>> case of the single precision simulation.
>>>> 
>>>> Did I do something wrong*? Any remarks are welcomed! I join the
>>> ‘mdout.mdp’
>>>> file so you can check what mdp options I used.
>>> 
>>> Maybe. Unfortunately we cannot configure the mailing list to allow people
>>> to send attachments to thousands of people, so you will need to do
>>> something like provide links to files on a sharing service.
>>> 
>>>> 
>>>> My second question is: if I did not do something wrong, what are the
>>>> consequences on the simulation? Can I trust the results of single
>>> precision
>>>> simulations?
>>> 
>>> Yes, as you have no doubt read in the papers published by the GROMACS
>> team.
>>> 
>>>> Regards,
>>>> 
>>>> Guillaume
>>>> 
>>>> *PS: I am not the only one encountering this behavior. In the
>> literature,
>>>> this problem has already been mentioned:
>>>> http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1
>>> 
>>> ... which is six years old, examining the properties of code seven years
>>> old. Life has moved on! :-) Even if you have found a problem, it is a big
>>> assumption that this is (still) the cause.
>>> 
>>> Mark
>>> 
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