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." Sorry for typos. Best, Nadir -----Original Message----- From: "CIHAN NADIR KAPLAN" <[EMAIL PROTECTED]> To: gmx-users@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@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
