Free energy of a protein.

Guest -

10:19:25 PM PST - Mon, Mar 7th 2011

Hello I'm trying to calculate the free energy of PDB file, with something like:
title "calculate free energy"
start FreeMD
prepare
print high
system gibbs_free
source model11.pdb
new_top new_seq
new_rst
center
orient
solvate box 10.0 20.0 30.0
free
update lists
end
task prepare
md

system gibbs_free

sd 100

end
task md optimize
task shell "cp gibbs_free.qrs gibbs_free.rst"
md

system gibbs_md

reference gibbs_free.qrs

noshake solute

print energies

end

task md energy
The error is "0: Failed to allocate scratch array smr4", a version without copying the rst file "could not open rst file". Would you give me some pointers on how to calculate the free energy of a protein.
Thanks

Guest -

8:45:36 AM PST - Fri, Mar 11th 2011
'Failed to allocate' error messages point to not having sufficient memory to allocate the needed arrays. You should include a memory card in the input deck specifying the amount of memory to be used by NWChem. If you do not provide a restart file, you will always get the "could not open rst file" message. Reading this file is done before allocating memory, as the size of arrays needed depend on what is read from the input, topology and restart files. Be aware that for the MD module, most of the memroy is in local arrays, and not in global arrays.

Guest -

11:22:51 AM PST - Sat, Mar 12th 2011
Thanks for your help. I'll give it a go. Much appreciated.

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