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

Mario Fernández Pendás mariofp77 at gmail.com
Mon Dec 15 12:57:09 CET 2014

Hi Justfin,

First of all, thank you very much for your answer.

At this point I am not running any particular simulation (that is why I
said that I am not thinking in using any constraint algorithm, I am not
concerned in solving practical problems by now), I am just trying to
understand completely what is the theory behind this check_bonds_timestep()
This is why I am asking how it is obtained explicitly that 4.44 number.

I hope my question is more clear now.

Thank you very much.

Best regards,

2014-12-14 2:15 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> On 12/13/14 11:34 AM, Mario Fernández Pendás wrote:
>> 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.
> As the comments at the top of check_bonds_timestep() note, it is not a
> check for the validity of the integration, more like a guideline to prevent
> people from incompatible settings.  If you are not using constraints, the
> upper limit of dt is likely 1 fs, but depending on what you're simulating,
> you may have to use a much lower value.  A few trial runs to check energy
> conservation and stability would likely solve this very quickly.
> -Justin
>  Thank you very much.
>> Best regards,
>> Mario
>> El 11/12/2014 18:20, "Mario Fernández Pendás" <mariofp77 at gmail.com>
>> escribió:
>>  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
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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