[gmx-users] Energy Minimisation

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> *Dear all,
>              I am trying to minimize the energy of the single molecule 
> using gromacs. I tried with the following mdp
> 
> ; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE
> include                  =
> define                   =
> 
> ; RUN CONTROL PARAMETERS
> integrator               = steep
> nsteps                   = 5000
> init_step                =
> 
> ; ENERGY MINIMIZATION OPTIONS
> emtol                    = 10
> emstep                   = 0.01
> nstcgsteep               =
> nbfgscorr                =
> nstcheckpoint            = 100
> nstlog                   = 100
> nstenergy                = 1
> 
> ; SIMULATED ANNEALING
> annealing                      = no
> annealing_npoints        =
> annealing_time             =
> annealing_temp            =
>  
> But it shows the following error,
>                                                   ERROR: The cut-off 
> length is longer than half the shortest box vector or
>  longer than the smallest box diagonal element. Increase the box size or 
> decrease rlist.
> 
>  I have not included any the cut-off in the mdp file, but it still shows 
> the error. Am I supposed to include something to mdp to run single 
> molecule energy minimisation.
> 

You should explicitly provide the settings you wish to use.  The default of 1.0 
nm will be applied (which may or may not be appropriate), and the error suggests 
your box is too small, so you should build a proper one.

http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist

-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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