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

[David van der Spoel]

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
> 
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++