Print MM optimized region?
Just Got Here
3:22:59 PM PDT - Wed, Aug 22nd 2012
Hello,

I'm finding that xyz foomm fooqm does not print the MM geometry.

The subsequent restart files (sys.002.rst sys.003.rst) are identical except for the QM region.

Is there something wrong in my analysis input?...



start sys
memory stack 800 mb heap 100 mb global 800 mb
prepare
system sys_ref
read sys.002.rst
write sys_md2.pdb
end

task prepare




My QM/MM job is set up like this:


md
system sys_ref
msa 1000
end

qmmm
eref 0.0
bqzone 9.0
region mm qm
maxiter 1000 15
ncycles 1000
density espfit
xyz foomm fooqm
end

task qmmm dft energy
task qmmm dft optimize


I would really like to see how the MM part (sidechain residues of a protein) is optimizing, and to ensure that it is actually being optimized.

Thank you in advance!

Clicked A Few Times
7:06:08 AM PDT - Fri, Oct 26th 2012
The format of rst file?
Hi,

I am trying to print MM region information using the same command as you, i.e. "xyz foomm fooqm“, but it does not work.

In NWChem 5.1.1 user documentation, the chapter 38 provides us some file formats, including segment file, sequence file etc, but it does not tell us the rst file format. There is no doubt that rst file is very important. I think it should include the coordinate information of MM region. As you say, "The subsequent restart files (sys.002.rst sys.003.rst) are identical except for the QM region." This means what?

Jingbo


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