[gmx-users] 1-4 interaction not within cut-off

[Justin A. Lemkul]

Rabab Toubar wrote:
> Hi,
> 
> I set my .mdp file to minimize the system for 1000 steps, but it stopped 
> at ~200 saying: "Stepsize too small, or no change in energy.
> Converged to machine precision, but not to the requested precision Fmax 
> < 10" but the molecule is now outside the box
> 

This is not really a problem, provided that both the potential energy and Fmax 
that resulted are 
reasonable.http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

> I did position restraint for 2ns using LINCS, and things went well
> 
> running md, it ran for only 0.3 ns out of 30, and I got an error message 
> that 1-4 interaction between 2 atoms are at a distance > table-size 
> (1nm) with a suggestion to increase the table-extension in mdp file.
> I checked  
> http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off 
> suggesting reminimizing.
> 

The other possibility is that your .mdp settings are inappropriate, but you 
haven't provided that information.

> My question is: is it OK that the system doesn't minimize till the end 
> of the specified number of steps? is it OK to be outside the box as long 
> as you assign boundary conditions as in case of NAMD? and what is the 
> best option - you think - I have to solve the md problem
> 

Whether or not you need to revisit the EM procedure depends on how well it 
actually did (see comment above).  The periodicity effect is a non-issue, since 
there is no "outside" of a periodic box.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> Any suggestions are highly apprecitaed
> Rabab
> 
> 

-- 
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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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