[gmx-users] basic units: acceleration conflict (revision)
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jun 14 16:13:03 CEST 2008
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
> Sorry for typos.
> -----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.
> Nadir Kaplan
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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