[gmx-users] problem with energy minimization after g_cluster

[Justin A. Lemkul]

DimitryASuplatov wrote:
> Hello,
> I have created a consensus structure from the last ns of my trajectory
> using g_cluster with default parameters and -av for writing average
> structure.
> When I am trying to energy minimize output structure with steep I get a
> non-sense result - 
> 
>    Tolerance (Fmax)   =  2.00000e+02
>    Number of steps    =         3000
> Step=   17, Dmax= 1.5e-06 nm, Epot=  1.51233e+18 Fmax=         inf,
> atom= 11754
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 200
> 
> This problem does not occur when using g_cluster without -av averaging -
> minimization performs as usual with a conversion in about 1000 steps.
> 
> Inspecting and comparing averaged and non-averaged structures I`ve found
> that 760 Leu (the one that is reported to have the highest energy) is
> corrupt - averaging creased the sidechain atoms to about two or three
> positions (I mean that several atoms overlap).
> Is that some kind of bug?

Have a look here:

http://wiki.gromacs.org/index.php/Average_Structure

-Justin

> Thanks.
> 
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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