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 manually.
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.
pb.
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/
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
On Jun 17, 2006, at 5:06 AM, Mahnam wrote:
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
