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" <[EMAIL PROTECTED]>
To: [email protected]
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.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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