[gmx-users] Makeing CPMD_inp.run

Pradip Kumar Biswas p.biswas at csuohio.edu
Sat Jun 17 18:19:01 CEST 2006

Hi Mahnam,

> 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
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
On Jun 17, 2006, at 5:06 AM, Mahnam wrote:

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