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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--
========================================
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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