[gmx-users] a warning in grompp

[Justin A. Lemkul]

Banafsheh Mehrazma wrote:
> dear all;
> I am trying to run grompp command and I encounter this:
>  
> .............................................................................
> WARNING 1 [file topol.top, line 54]:
>   The bond in molecule-type DNA_chain_A between atoms 1 H5T and 2 O5' has
>   an estimated oscillational period of 9.0e-03 ps, which is less than 5
>   times the time step of 2.0e-03 ps.
>   Maybe you forgot to change the constraints mdp option.
> ................................................................................
>  however when I use -maxwarn with grompp, it seems like that there is 
> nothing wrong. Is it OK to continue the simulation with using maxwarn, 
> or is there some thig wrong that needs to be modified?
> 

Don't believe that nothing is wrong when using -maxwarn.  If you're invoking 
-maxwarn, you're telling grompp "ignore all the things you think are problems." 
  Unless you understand the exact implications of overriding these warnings, you 
shouldn't be blindly pushing forward.  As the warning states, your time step is 
too long to be stable in the absence of constraints.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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