Thank you for your answer Mark. I was not able to find this information in manual. If it is present, could you please refer me to the relevant section. If it is indeed not there, it would be very helpful to include it in the manual.
Sincerely, Ravi Bhadauria On Thu, Nov 10, 2011 at 6:18 AM, Mark Abraham <[email protected]> wrote: > On 9/11/2011 9:44 PM, Ravi Bhadauria wrote: >> >> Hello users, >> >> I have few conflicting answers from the user mailing list about the >> following question. >> >> Using leap-frog integrator, what is the velocity that is WRITTEN in >> the trajectory file for a frame corresponding to r(t)? Is it v(t-dt/2) >> or v(t). Has the protocol for writing velocity in trajectory file been >> consistent from version 3.x to 4.5.x? > > With leap-frog, it is v(t-dt/2) in 4.5.x. v(t) is never even computed (see > do_update_md() in src/mdlib/update.c). I don't know if Erik's statement was > accurate in 2002, but it isn't accurate now. > > Mark > >> >> Here are few posts hinting its v(t): >> http://lists.gromacs.org/pipermail/gmx-users/2002-July/001969.html >> http://lists.gromacs.org/pipermail/gmx-users/2003-September/006956.html >> >> Here are couple of posts hinting its v(t-dt/2): >> http://lists.gromacs.org/pipermail/gmx-users/2006-June/022261.html >> http://lists.gromacs.org/pipermail/gmx-users/2003-March/004827.html >> >> Please let me know. The problem is with certain class of simulations >> of bounded flows, these two definitions provide contrasting results >> for suitably averaged velocity. >> >> Sincerely >> Ravi Bhadauria > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
