[gmx-users] Makeing CPMD_inp.run
Pradip Kumar Biswas
p.biswas at csuohio.edu
Sat Jun 17 18:19:01 CEST 2006
> In God We Trust
> Hello Dr Biswas
> Thank you very much for your reply.
> We are working with Gromos force field by QMMM_GMX for QMMM
> minimization of bilirubin at HSA.
> 1-How can we add non-polar hydrogens to united atoms in QM box
> of bilirubin?
> 2-How can we make CPMD_int.run and in section atoms and how can we
> calculate coordinates for each atoms for bilirubin molecule?
All the atom id's mentioned in the section [QM] of the index file
index.ndx will be automatically included in the QM system. The rest of
the atoms will be included in the external electric filed section
"EXTELEC" (Bond breaking and addition of link atoms for the QM system
is automatically done inside the code but it is now restricted to cut
accross C-C bond only; you can add additionals if you need). Once you
create a section [QM] with your required QM atoms, the program will
automatically generate CPMD_inp.run; you don't need to create it
> 3-May I ask you to explain EXTELEC section in your examples?
EXTELEC section contains atoms that are not part of the QM system. It
is now divided into three layers: innermost, intermediate, and outer
with an intention to get some adiabatic correction of energy of forces
for the intermediate and outer layers. At this point, I suggest you to
use only the innermost layer and set its radius as the QMMM_Coulomb
cutoff. Use the following type for grompp setup:
qmmmcoul_cutoff = 10
qmbox_cpmd = 45.0 40.0 35.0
MMlayer_radii = 10 10
Here the inner layer radius, the intermediate layer radius, and the
Coulomb cutoff are all set to 10A. Note that all the atoms within 10A,
surrounding any QM atom will be in this innermost layer; in addition
all the charge residues will also be in this innermost layer
irrespective of their distances. Use the appropriate box size replacing
45.0(=dx), 40.0(=dy), and 35.0(=dz) in Angstrom;
> 4-It seems that QM box at your examples is more than space between the
> outermost atoms plus 3 angstrom?. How can we select QM box dimensions
> for bilirubin?
Look at the output file output.mdrun_xx (xx=nm,md); there you would
find the print of the size of the QM system as "QM bounding box" before
CPMD starts. Now, you need a "QM simulation box" within which the
wavefunction of the QM system will converge. This should come from
experience. In general, you can start taking a simulation box size that
extends at least about 3-4 Angstrom beyond the boundary of the QM
system. Not that it also depends on the planewave cutoff; with a higher
cutoff you can take a lower box size.
> Thank you very much in advance..
> Sincerely yours
> Karim Mahnam
> Institute of Biochemistry and Biophysics (IBB)
> Tehran University
> P.O.box 13145-1384
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
On Jun 17, 2006, at 5:06 AM, Mahnam wrote:
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