Schrodinger is a scientific leader in computational chemistry, providing software solutions and services for life sciences and materials research.
This example illustrates using Schrodinger in a batch mode on the FASRC cluster at Harvard University. The specific example computes properties of water molecule using Jaguar.
(1) H20.in: Input data file
(2) run.sbatch: Batch job submission script for sending the job to the queue.
source new-modules.sh
module load schrodinger/2014.3-fasrc01
sbatch run.sbatch
The following files are generated after the job completes:
H2O.01.in H2O.01.mae H2O.log H2O.out test_water.err test_water.out
Below are contents of H2O.out:
[pkrastev@sa01 test2]$ cat H2O.out
Job H2O started on holy2a13308.rc.fas.harvard.edu at Fri Apr 29 14:41:59 2016
jobid: holy2a13308-0-5723aaf5
+--------------------------------------------------------------------+
| Jaguar version 8.5, release 13 |
| |
| Copyright Schrodinger, Inc. |
| All Rights Reserved. |
| |
| The following have contributed to Jaguar (listed alphabetically): |
| Mike Beachy, Art Bochevarov, Dale Braden, Yixiang Cao, |
| Chris Cortis, Rich Friesner, Bill Goddard, Hod Greeley, |
| Tom Hughes, Jean-Marc Langlois, Daniel Mainz, Rob Murphy, |
| Dean Philipp, Tom Pollard, Murco Ringnalda. |
| |
| Use of this program should be acknowledged in publications as: |
| |
| Jaguar, version 8.5, Schrodinger, Inc., New York, NY, 2014. |
| |
| A. D. Bochevarov, E. Harder, T. F. Hughes, J. R. Greenwood, |
| D. A. Braden, D. M. Philipp, D. Rinaldo, M. D. Halls, |
| J. Zhang, R. A. Friesner, "Jaguar: A High-Performance Quantum |
| Chemistry Software Program with Strengths in Life and Materials |
| Sciences", Int. J. Quantum Chem., 2013, 113(18), 2110-2142. |
+--------------------------------------------------------------------+
start of program pre
--------echo of input .in file:-----------------
JOB: H2O
EXEC: /n/sw/schrodinger2014-3/jaguar-v85013/bin/Linux-x86_64
SCRATCH: /scratch/pkrastev/H2O
OUTPUT: /n/home06/pkrastev/workdirs/schrodinger/test2
RESTARTJOB: H2O.01
&gen
&
&echo
&
&zmat
O 0.0000000000000 0.0000000000000 -0.1135016000000
H1 0.0000000000000 0.7531080000000 0.4540064000000
H2 0.0000000000000 -0.7531080000000 0.4540064000000
&
MAEFILE: H2O.mae
------------end of .in file---------------------
Job name: H2O
Executables used: /n/sw/schrodinger2014-3/jaguar-v85013/bin/Linux-x86_64
Temporary files : /scratch/pkrastev/H2O
Maestro file (input): H2O.mae
Maestro file (output): H2O.01.mae
basis set: 6-31g**
net molecular charge: 0
multiplicity: 1
number of basis functions.... 25
Input geometry:
angstroms
atom x y z
O 0.0000000000 0.0000000000 -0.1135016000
H1 0.0000000000 0.7531080000 0.4540064000
H2 0.0000000000 -0.7531080000 0.4540064000
principal moments of inertia:
amu*angstrom^2: 0.57652 1.14322 1.71974
g*cm^2: 9.57332390E-41 1.89836056E-40 2.85569295E-40
rotational constants:
cm^(-1): 29.24036473 14.74574897 9.80243631
GHz: 876.60408151 442.06643298 293.86964764
Molecular weight: 18.01 amu
Stoichiometry: H2O
Molecular Point Group: C2v
Molecule translated to center of mass
Molecule reoriented along symmetry axes
Point Group used: C2v
Symmetrized geometry:
angstroms
atom x y z
O 0.0000000000 0.0000000000 -0.0635125859
H1 0.0000000000 0.7531080000 0.5039954141
H2 0.0000000000 -0.7531080000 0.5039954141
nuclear repulsion energy....... 9.330006048 hartrees
Non-default options chosen:
Temporary integer options set:
73= 2
Peak memory usage: 520 Mb
end of program pre
Time(pre) user: 0.2 user+sys: 0.2 wallclock: 1.9
start of program onee
smallest eigenvalue of S: 1.979E-02
number of canonical orbitals..... 25
Peak memory usage: 660 Mb
end of program onee
Time(onee) user: 0.2 user+sys: 0.2 wallclock: 0.3
start of program hfig
initial wavefunction generated automatically from atomic wavefunctions
Irreducible Total no No of occupied orbitals
representation orbitals Shell_1 Shell_2 ...
A1 12 3
A2 2 0
B1 4 1
B2 7 1
------------------------
Orbital occupation/shell 1.000
Peak memory usage: 599 Mb
end of program hfig
Time(hfig) user: 0.1 user+sys: 0.1 wallclock: 0.3
start of program probe
Peak memory usage: 599 Mb
end of program probe
Time(probe) user: 0.1 user+sys: 0.1 wallclock: 0.3
start of program grid
grid grid set grid # grid sym
------ -------- ------ --------
coarse 0 0 1
medium 2 1 4
fine 0 0 1
ultrafine 4 2 4
charge 0 0 1
gradient 4 2 4
density 0 0 1
DFT-fine 0 0 1
DFT-med. 0 0 1
DFT-grad 0 0 1
DFT-der2 0 0 1
DFT-cphf 0 0 1
LMP2-enrg 4 2 4
LMP2-grad 2 1 4
DFT-cphf2 0 0 1
PBF-dens 0 0 1
plotting 0 0 1
Rel-grad -17 0 1
number of gridpoints:
atom O H1 H2 total
grid # 1 40 69 0 109
grid # 2 140 263 0 403
Peak memory usage: 617 Mb
end of program grid
Time(grid) user: 0.1 user+sys: 0.1 wallclock: 0.3
start of program rwr
Peak memory usage: 521 Mb
end of program rwr
Time(rwr) user: 0.2 user+sys: 0.2 wallclock: 0.3
start of program scf
number of electrons.......... 10
number of alpha electrons.... 5
number of beta electrons..... 5
number of orbitals, total.... 25
number of doubly-occ'd orbs.. 5
number of open shell orbs.... 0
number of occupied orbitals.. 5
number of virtual orbitals... 20
number of hamiltonians....... 1
number of shells............. 1
SCF type: HF
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -75.75389050468 1.3E-02 2.6E-01
etot 2 Y Y 6 M -76.00999984809 2.6E-01 3.2E-03 4.7E-02
etot 3 N Y 2 U -76.02240478774 1.2E-02 1.0E-03 1.7E-02
etot 4 Y Y 6 M -76.02340960900 1.0E-03 3.9E-04 5.3E-03
etot 5 Y Y 6 M -76.02355192636 1.4E-04 1.3E-04 9.7E-04
etot 6 N Y 2 U -76.02360634202 5.4E-05 3.6E-05 2.5E-04
etot 7 N N 2 U -76.02360707695 7.3E-07 0.0E+00 0.0E+00
Energy components, in hartrees:
(A) Nuclear repulsion............ 9.33000604793
(E) Total one-electron terms..... -123.34015789160
(I) Total two-electron terms..... 37.98654476672
(L) Electronic energy............ -85.35361312488 (E+I)
(N) Total energy................. -76.02360707695 (A+L)
SCFE: SCF energy: HF -76.02360707695 hartrees iterations: 7
HOMO energy: -0.49762
LUMO energy: 0.21539
Orbital energies (hartrees)/symmetry label:
-20.55723 A1 -1.34648 A1 -0.71401 B2 -0.56819 A1
-0.49762 B1 0.21539 A1 0.30812 B2 1.01702 B2
1.09293 A1 1.13455 A1 1.16897 B1 1.29525 B2
1.41155 A1 1.80246 A2 1.82987 A1
Peak memory usage: 740 Mb
end of program scf
Time(scf) user: 0.3 user+sys: 0.3 wallclock: 0.6
Total cpu seconds user: 0.401 user+sys: 0.401
Total elapsed time: 8 seconds
Job H2O completed on holy2a13308.rc.fas.harvard.edu at Fri Apr 29 14:42:07 2016
- Official Scrodinger documentation
- [Jaguar documentation (release 2014-3)] (https://hpc.nih.gov/apps/schrodinger/docs-2014-3/jaguar/jaguar_user_manual.pdf)