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 <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@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" <[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 -- 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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 _______________________________________________ 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. 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