[gmx-users] basic units: acceleration conflict (revision)

Sun Jun 15 10:50:01 CEST 2008

Hi Nadir,

First of all, nm / ps^2 for acceleration was not a choice, but a
consequence of other choices. Second, it's meaningless to pull this
out of context. There's no reason whatsoever not to have a huge
accelaration, if it is only for short times. It's the speed that
counts, not the acceleration. E.g. given an electric field
(condensator plates?) and a charged species (hydronium, to stick close
to your water?), I think it would be possible to boost up to force
acting on the ion, giving it an acceleration close to what you say
here is unphysical. But the acceleration would only last for a very
short period. It won't take two seconds before the molecule bashes
into the oppsite plate.
By the way, can you imagine a simulation of a box of water with an
acceleration applied, for a simulated time of 2 seconds?

Still, your concern may be valid, but you will have to demonstrate
then that the velocities reached in the end, or the forces (electric
fields) required to achieve such accelerations are unphysical, rather
than referring to the accelerations themselves.

Cheers,

Tsjerk

On Sat, Jun 14, 2008 at 10:34 PM, CIHAN NADIR KAPLAN <CIKAPLAN at ku.edu.tr> wrote:
> I rewrite the mail using words instead of numbers:
>
> ************
>
> In the Gromacs manual, the basic units for length and time are given by nm(=ten to the minus nine meter) and ps(=ten to the minus twelve seconds), respectively. When one wants to accelerate a group, he should include it in the *.mdp file in the units of nm/(ps squared), which corresponds to ten to fifteen meter/(second squared). So , for instance, when you set the acceleration in x direction greater than approximately ten to minus seven in the mdp file, then according to given units, it is unphysical. Even, in order to avoid relativistic effects, it seems it should be set less than approximately ten to minus ten, but the manual says "GROMACS uses a consistent set of units that produce values in the vicinity of unity for most relevant molecular quantities" (page seven).
>
> Can anyone please explain the logic behind choosing nm/(ps sqaured) ? Any help will be greatly appreciated.
>
> **************
>
>
> But it doesn't crash. Let me tell the simulation setup: You have a carbon nanotube, you put it in a box with water, initially v= zero for all water molecules, you freeze the tube and let molecules experience an external acceleration of 0.002 nm/(ps squared) (if the number is unreadable, it is "zero point zero zero two") in the axial direction of the tube. So at the end, when you look into trr or gro file which is produced by mdrun, you may see velocities of water molecules (let's say oxygen for simplicity) such as -2.6745 or 0.2220, etc. (in words: minus two point six seven four five and zero point two two two zero, respectively) and those results are real.
>
> Let me summarize the conflict in this example:
> The acceleration to be applied corresponds to 2x10^12 meter/(second squared) (in words: two times ten to twelve) which means in vacuum that water molecule may gain two times ten to twelve meter/second velocity at every second (e.g. for dilute case). And in the end, the velocities are:  2.6745 km/s or 0.2220 km/s. (in words: minus two point six seven four five kilometer/second and zero point two two two zero kilometer/second, respectively). Can you imagine a water molecule which goes with a velocity of two kilometer per second?
>
> Such results are everywhere (also in journals) ...
>
> I still hope that I underestimate something or don't take an important point into account. Please help...
>
> Best,
> Nadir
>
> -----Original Message-----
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sat, 14 Jun 2008 16:13:03 +0200
> Subject: Re: [gmx-users] basic units: acceleration conflict (revision)
>
> CIHAN NADIR KAPLAN wrote:
>> There has been some typos.
>>
>> I mean, such an acceleration would result in unphysical velocities since the relativistic effects are not accounted.
>> The passage in question should be as follows:
>>
>> "When one wants to accelerate a group, he should include it in the *.mdp file in the units of nm/ps^2, which corresponds to 10^15 m/s^2. So , for instance, when you set the acceleration in x direction greater than ~10^-7 in the mdp file, then according to given units, it is not physical."
>>
> Unfortunately the numbers in your emails are unreadable for me. But the
> velocities are usually not relativistic. Although you could of course
> reach velocities larger then c in a classical program :). mdrun would
> crash though...
>
>> Sorry for typos.
>>
>> Best,
>> Nadir
>>
>> -----Original Message-----
>> From: "CIHAN NADIR KAPLAN" <CIKAPLAN at KU.EDU.TR>
>> To: gmx-users at gromacs.org
>> Date: Sat, 14 Jun 2008 13:30:10 +0300
>> Subject: basic units: acceleration conflict
>>
>> Dear all,
>>
>> In the Gromacs manual, the basic units for length and time are given by nm(=10^-9 m) and ps(=10^-12s), respectively. When one wants to accelerate a group, he should include it in the *.mdp file in the units of nm/ps^2, which corresponds to 10^15 m/s. So , for instance, when you set the acceleration in x direction greater than ~10^-7 in the mdp file, then according to given units, it is not unphysical. Even, in order to avoid relativistic effects, it seems it should be set less than ~10^-9, but the manual says "GROMACS uses a consistent set of units that produce values in the vicinity of unity for most
>> relevant molecular quantities" (p.7).
>>
>> Can anyone please explain the logic behind choosing nm/ps^2 ? Any help will be greatly appreciated.
>>
>> Best,
>> Nadir Kaplan
>>
>>
>>
>>
>>
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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