[gmx-users] about the velocity output from leap-frog integrators

Ravi Bhadauria leoravs at gmail.com
Fri Nov 11 05:21:19 CET 2011

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.

Ravi Bhadauria

On Thu, Nov 10, 2011 at 6:18 AM, Mark Abraham <Mark.Abraham at anu.edu.au> 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
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