[gmx-users] Maximun time-step recommended in the grompp part for each system

Mario Fernández Pendás mariofp77 at gmail.com
Sat Dec 13 17:34:15 CET 2014

Some extra information about this topic:

We are exicitely interested in NOT using any kind of constraints. As you
may assume, the purpose of this study is purely theoretical.

Thank you very much.

Best regards,
El 11/12/2014 18:20, "Mario Fernández Pendás" <mariofp77 at gmail.com>

> Dear all,
> Taking look at the check_bonds_timestep() function in src/kernel/grompp.c
> used for checking the time-step used for the integration of the equations
> of motion a few questions come to me:
> - In the comments of the function it is said that "The stability limit of
> leap-frog or velocity verlet is 4.44 steps per oscillational period". Does
> anyone know how this exact number is obtained?
> - I see that, inside of the function, there are two "limits": 5 and 10.
> They are used for establishing a relation between the estimated oscillation
> period of the bond between two atoms of the system in use and the time-step
> used for integrating the equations of motion and giving a warning message
> in case of using a non suitable time-step. I assume, looking at the
> literature, that this limits are taking from the following paper by Mazur:
> http://www.sciencedirect.com/science/article/pii/S0021999197957405
> Am I right?
> I have also found an issue in redmine for the function
> check_bonds_timestep() reporting that it only reports the first suspicious
> bond. I think this does not affect my questions.
> Thank you very much.
> Best regards,
> Mario

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