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## NAMD
[NAMD](http://www.ks.uiuc.edu/Research/namd) is a parallel molecular
dynamics code designed for high-performance simulation of large
biomolecular systems.
The current version in modenv/scs5 can be started with srun as usual.
Note that the old version from modenv/classic does not use MPI but
rather uses Infiniband directly. Therefore, you cannot not use
srun/mpirun to spawn the processes but have to use the supplied
"charmrun" command instead. Also, since this is batch system agnostic,
it has no possiblity of knowing which nodes are reserved for it use, so
if you want it to run on more than node, you have to create a hostlist
file and feed it to charmrun via the parameter "++nodelist". Otherwise,
all processes will be launched on the same node (localhost) and the
other nodes remain unused.
You can use the following snippet in your batch file to create a
hostlist file:
export NODELISTFILE="/tmp/slurm.nodelist.$SLURM_JOB_ID"
for LINE in `scontrol show hostname $SLURM_JOB_NODELIST` ; do
echo "host $LINE" >> $NODELISTFILE ;
done
# launch NAMD processes. Note that the environment variable $SLURM_NTASKS is only available if you have
# used the -n|--ntasks parameter. Otherwise, you have to specify the number of processes manually, e.g. +p64
charmrun +p$SLURM_NTASKS ++nodelist $NODELISTFILE $NAMD inputfile.namd
# clean up afterwards:
test -f $NODELISTFILE && rm -f $NODELISTFILE
The current version 2.7b1 of NAMD runs much faster than 2.6. -
Especially on the SGI Altix. Since the parallel performance strongly
depends on the size of the given problem one cannot give a general
advice for the optimum number of CPUs to use. (Please check this by
running NAMD with your molecules and just a few time steps.)
Any published work which utilizes NAMD shall include the following
reference: \<br /> *James C. Phillips, Rosemary Braun, Wei Wang, James
Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D.
Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics
with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005.*
Electronic documents will include a direct link to the official NAMD
page at <http://www.ks.uiuc.edu/Research/namd/>
[NAMD](http://www.ks.uiuc.edu/Research/namd) is a parallel molecular dynamics code designed for
high-performance simulation of large biomolecular systems.
## Gaussian
The current version in modenv/scs5 can be started with `srun` as usual.
Starting from the basic laws of quantum mechanics,
[Gaussian](http://www.gaussian.com) predicts the energies, molecular
structures, and vibrational frequencies of molecular systems, along with
numerous molecular properties derived from these basic computation
types. It can be used to study molecules and reactions under a wide
range of conditions, including both stable species and compounds which
are difficult or impossible to observe experimentally such as
short-lived intermediates and transition structures.
Note that the old version from modenv/classic does not use MPI but rather uses Infiniband directly.
Therefore, you cannot not use srun/mpirun to spawn the processes but have to use the supplied
"charmrun" command instead. Also, since this is batch system agnostic, it has no possiblity of
knowing which nodes are reserved for it use, so if you want it to run on more than node, you have to
create a hostlist file and feed it to charmrun via the parameter "++nodelist". Otherwise, all
processes will be launched on the same node (localhost) and the other nodes remain unused.
With `module load gaussian` (or `gaussian/g09`) a number of environment
variables are set according to the needs of Gaussian. Please, set the
directory for temporary data (GAUSS_SCRDIR) manually to somewhere below
\<span>/scratch (you get the path, when you generated a workspace for
your calculation)\<br />\</span>
You can use the following snippet in your batch file to create a hostlist file:
This is a small example, kindly provide by Arno Schneeweis (Inst. fr
Angewandte Physik). You need a batch file - for example called
"mybatch.sh" with the following content:
```Bash
export NODELISTFILE="/tmp/slurm.nodelist.$SLURM_JOB_ID"
for LINE in `scontrol show hostname $SLURM_JOB_NODELIST` ; do
echo "host $LINE" >> $NODELISTFILE ;
done
#!/bin/bash<br />#SBATCH --nodes=1<br />#SBATCH --ntasks-per-node=4 # this number of CPU's has to match with the %nproc in the inputfile<br />#SBATCH --mem=4000<br />#SBATCH --time=00:10:00 # hh:mm:ss<br />#SBATCH --mail-type=END,FAIL<br />#SBATCH --mail-user=vorname.nachname@tu-dresden.de<br />#SBATCH -A ...your_projectname... <br /><br />#### make available the access to Gaussian 16<br />module load modenv/classic<br />module load gaussian/g16_avx2<br />export GAUSS_SCRDIR=...path_to_the_Workspace_that_you_generated_before...<br />g16 &lt; my_input.com &gt; my_output.out
# launch NAMD processes. Note that the environment variable $SLURM_NTASKS is only available if you have
# used the -n|--ntasks parameter. Otherwise, you have to specify the number of processes manually, e.g. +p64
charmrun +p$SLURM_NTASKS ++nodelist $NODELISTFILE $NAMD inputfile.namd
*As example the input for gaussian could be this my_input.com:\<br />*
# clean up afterwards:
test -f $NODELISTFILE && rm -f $NODELISTFILE
```
%mem=4GB<br />%nproc=4<br />#P B3LYP/6-31G* opt<br /><br />Toluol<br /><br />0 1<br />C 1.108640 0.464239 -0.122043<br />C 1.643340 -0.780361 0.210457<br />C 0.794940 -1.850561 0.494257<br />C -0.588060 -1.676061 0.445657<br />C -1.122760 -0.431461 0.113257<br />C -0.274360 0.638739 -0.170643<br />C -0.848171 1.974558 -0.527484<br />H 1.777668 1.308198 -0.345947<br />H 2.734028 -0.917929 0.248871<br />H 1.216572 -2.832148 0.756392<br />H -1.257085 -2.520043 0.669489<br />H -2.213449 -0.293864 0.074993<br />H -1.959605 1.917127 -0.513867<br />H -0.507352 2.733596 0.211754<br />H -0.504347 2.265972 -1.545144<br /><br />
The current version 2.7b1 of NAMD runs much faster than 2.6. - Especially on the SGI Altix. Since
the parallel performance strongly depends on the size of the given problem one cannot give a general
advice for the optimum number of CPUs to use. (Please check this by running NAMD with your molecules
and just a few time steps.)
You have to start the job with command:
Any published work which utilizes NAMD shall include the following reference:
sbatch mybatch.sh
*James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe
Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005.*
## \<a name="gamess">\</a>GAMESS US
Electronic documents will include a direct link to the official NAMD page at
http://www.ks.uiuc.edu/Research/namd
GAMESS is an ab-initio quantum mechanics program, which provides many
methods for computation of the properties of molecular systems using
standard quantum chemical methods. For a detailed description, please
look at the [GAMESS home
page](http://www.msg.ameslab.gov/GAMESS/GAMESS.html).
## Gaussian
For runs with Slurm, please use a script like this:
Starting from the basic laws of quantum mechanics, [Gaussian](http://www.gaussian.com) predicts the
energies, molecular structures, and vibrational frequencies of molecular systems, along with
numerous molecular properties derived from these basic computation types. It can be used to study
molecules and reactions under a wide range of conditions, including both stable species and
compounds which are difficult or impossible to observe experimentally such as short-lived
intermediates and transition structures.
With `module load gaussian` (or `gaussian/g09`) a number of environment variables are set according
to the needs of Gaussian. Please, set the directory for temporary data (GAUSS_SCRDIR) manually to
somewhere below `/scratch` (you get the path, when you generated a workspace for your
calculation).
This is a small example, kindly provide by Arno Schneeweis (Inst. fr Angewandte Physik). You need a
batch file - for example called "mybatch.sh" with the following content:
```Bash
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4 # this number of CPU's has to match with the %nproc in the inputfile
#SBATCH --mem=4000
#SBATCH --time=00:10:00 # hh:mm:ss
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=vorname.nachname@tu-dresden.de
#SBATCH -A ...your_projectname...
####
make available the access to Gaussian 16
module load modenv/classic
module load gaussian/g16_avx2
export GAUSS_SCRDIR=...path_to_the_Workspace_that_you_generated_before...
g16 < my_input.com > my_output.out
```
*As example the input for gaussian could be this my_input.com:*
```Bash
%mem=4GB
%nproc=4
#P B3LYP/6-31G* opt
Toluol
0 1
C 1.108640 0.464239 -0.122043
C 1.643340 -0.780361 0.210457
C 0.794940 -1.850561 0.494257
C -0.588060 -1.676061 0.445657
C -1.122760 -0.431461 0.113257
C -0.274360 0.638739 -0.170643
C -0.848171 1.974558 -0.527484
H 1.777668 1.308198 -0.345947
H 2.734028 -0.917929 0.248871
H 1.216572 -2.832148 0.756392
H -1.257085 -2.520043 0.669489
H -2.213449 -0.293864 0.074993
H -1.959605 1.917127 -0.513867
H -0.507352 2.733596 0.211754
H -0.504347 2.265972 -1.545144
```
#!/bin/bash<br />#SBATCH -t 120<br />#SBATCH -n 8<br />#SBATCH --ntasks-per-node=2<br /># you have to make sure that on each node runs an even number of tasks !!<br />#SBATCH --mem-per-cpu=1900<br />module load gamess<br />rungms.slurm cTT_M_025.inp /scratch/mark/gamess <br /># the third parameter is the location of the scratch directory<br />
You have to start the job with command:
*GAMESS should be cited as:* M.W.Schmidt, K.K.Baldridge, J.A.Boatz,
S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen,
S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery, J.Comput.Chem. 14,
1347-1363(1993).
```Batch
sbatch mybatch.sh
```
## GAMESS US
## \<a name="lammps">\</a>LAMMPS
GAMESS is an ab-initio quantum mechanics program, which provides many methods for computation of the
properties of molecular systems using standard quantum chemical methods. For a detailed description,
please look at the [GAMESS home page](http://www.msg.ameslab.gov/GAMESS/GAMESS.html).
[LAMMPS](http://lammps.sandia.gov) is a classical molecular dynamics
code that models an ensemble of particles in a liquid, solid, or gaseous
state. It can model atomic, polymeric, biological, metallic, granular,
and coarse-grained systems using a variety of force fields and boundary
conditions. For examples of LAMMPS simulations, documentations, and more
visit [LAMMPS sites](http://lammps.sandia.gov).
For runs with Slurm, please use a script like this:
```Bash
#!/bin/bash
#SBATCH -t 120
#SBATCH -n 8
#SBATCH --ntasks-per-node=2
# you have to make sure that on each node runs an even number of tasks !!
#SBATCH --mem-per-cpu=1900
module load gamess
rungms.slurm cTT_M_025.inp /scratch/mark/gamess
# the third parameter is the location of the scratch directory
```
*GAMESS should be cited as:* M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon,
J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery,
J.Comput.Chem. 14, 1347-1363(1993).
## LAMMPS
[LAMMPS](http://lammps.sandia.gov) is a classical molecular dynamics code that models an ensemble of
particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological,
metallic, granular, and coarse-grained systems using a variety of force fields and boundary
conditions. For examples of LAMMPS simulations, documentations, and more visit
[LAMMPS sites](http://lammps.sandia.gov).
## ABINIT
[ABINIT](http://www.abinit.org) is a package whose main program allows
one to find the total energy, charge density and electronic structure of
systems made of electrons and nuclei (molecules and periodic solids)
within Density Functional Theory (DFT), using pseudopotentials and a
planewave basis. ABINIT also includes options to optimize the geometry
according to the DFT forces and stresses, or to perform molecular
dynamics simulations using these forces, or to generate dynamical
matrices, Born effective charges, and dielectric tensors. Excited states
can be computed within the Time-Dependent Density Functional Theory (for
molecules), or within Many-Body Perturbation Theory (the GW
approximation).
[ABINIT](http://www.abinit.org) is a package whose main program allows one to find the total energy,
charge density and electronic structure of systems made of electrons and nuclei (molecules and
periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave
basis. ABINIT also includes options to optimize the geometry according to the DFT forces and
stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical
matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the
Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory
(the GW approximation).
## CP2K
[CP2K](http://cp2k.berlios.de/) performs atomistic and molecular
simulations of solid state, liquid, molecular and biological systems. It
provides a general framework for different methods such as e.g. density
functional theory (DFT) using a mixed Gaussian and plane waves approach
(GPW), and classical pair and many-body potentials.
[CP2K](http://cp2k.berlios.de/) performs atomistic and molecular simulations of solid state, liquid,
molecular and biological systems. It provides a general framework for different methods such as e.g.
density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical
pair and many-body potentials.
## CPMD
The CPMD code is a plane wave/pseudopotential implementation of Density
Functional Theory, particularly designed for ab-initio molecular
dynamics. For examples and documentations see [CPMD
homepage](http://www.cpmd.org).
The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory,
particularly designed for ab-initio molecular dynamics. For examples and documentations see
[CPMD homepage](http://www.cpmd.org).
## GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e.
simulate the Newtonian equations of motion for systems with hundreds to
millions of particles. It is primarily designed for biochemical
molecules like proteins, lipids and nucleic acids that have a lot of
complicated bonded interactions, but since GROMACS is extremely fast at
calculating the nonbonded interactions (that usually dominate
simulations) many groups are also using it for research on
non-biological systems, e.g. polymers.
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations
of motion for systems with hundreds to millions of particles. It is primarily designed for
biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded
interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that
usually dominate simulations) many groups are also using it for research on non-biological systems,
e.g. polymers.
For documentations see [Gromacs homepage](http://www.gromacs.org/).
## ORCA
ORCA is a flexible, efficient and easy-to-use general purpose tool for
quantum chemistry with specific emphasis on spectroscopic properties of
open-shell molecules. It features a wide variety of standard quantum
chemical methods ranging from semiempirical methods to DFT to single-
and multireference correlated ab initio methods. It can also treat
environmental and relativistic effects.
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with
specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of
standard quantum chemical methods ranging from semiempirical methods to DFT to single- and
multireference correlated ab initio methods. It can also treat environmental and relativistic
effects.
To run Orca jobs in parallel, you have to specify the number of
processes in your input file (here for example 16 processes):
To run Orca jobs in parallel, you have to specify the number of processes in your input file (here
for example 16 processes):
%pal nprocs 16 end
```Bash
%pal nprocs 16 end
```
Note that Orca does the MPI process spawning itself, so you may not use
"srun" to launch it in your batch file. Just set --ntasks to the same
number as in your input file and call the "orca" executable directly.
For parallel runs, it must be called with the full path:
Note that Orca does the MPI process spawning itself, so you may not use "srun" to launch it in your
batch file. Just set --ntasks to the same number as in your input file and call the "orca"
executable directly. For parallel runs, it must be called with the full path:
#!/bin/bash
#SBATCH --ntasks=16
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=2000M
```Bash
#!/bin/bash #SBATCH --ntasks=16 #SBATCH --nodes=1 #SBATCH --mem-per-cpu=2000M
$ORCA_ROOT/orca example.inp
$ORCA_ROOT/orca example.inp
```
## Siesta
Siesta (Spanish Initiative for Electronic Simulations with Thousands of
Atoms) is both a method and its computer program implementation, to
perform electronic structure calculations and ab initio molecular
dynamics simulations of molecules and solids. <http://www.uam.es/siesta>
In any paper or other academic publication containing results wholly or
partially derived from the results of use of the SIESTA package, the
following papers must be cited in the normal manner: 1 "Self-consistent
order-N density-functional calculations for very large systems", P.
Ordejon, E. Artacho and J. M. Soler, Phys. Rev. B (Rapid Comm.) 53,
R10441-10443 (1996). 1 "The SIESTA method for ab initio order-N
materials simulation" J. M. Soler, E. Artacho, J. D. Gale, A. Garcia, J.
Junquera, P. Ordejon, and D. Sanchez-Portal, J. Phys.: Condens. Matt.
14, 2745-2779 (2002).
Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and
its computer program implementation, to perform electronic structure calculations and ab initio
molecular dynamics simulations of molecules and solids. <http://www.uam.es/siesta>
In any paper or other academic publication containing results wholly or partially derived from the
results of use of the SIESTA package, the following papers must be cited in the normal manner: 1
"Self-consistent order-N density-functional calculations for very large systems", P. Ordejon, E.
Artacho and J. M. Soler, Phys. Rev. B (Rapid Comm.) 53, R10441-10443 (1996). 1 "The SIESTA method
for ab initio order-N materials simulation" J. M. Soler, E. Artacho, J. D. Gale, A. Garcia, J.
Junquera, P. Ordejon, and D. Sanchez-Portal, J. Phys.: Condens. Matt. 14, 2745-2779 (2002).
## VASP
"VAMP/VASP is a package for performing ab-initio quantum-mechanical
molecular dynamics (MD) using pseudopotentials and a plane wave basis
set."
[\[http://cms.mpi.univie.ac.at/vasp/ Official Site]([http://cms.mpi.univie.ac.at/vasp/ Official Site)\].
It is installed on mars. If you are interested in using VASP on ZIH
machines, please contact [Dr. Ulf
"VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using
pseudopotentials and a plane wave basis set." [VASP](https://www.vasp.at). It is installed on mars.
If you are interested in using VASP on ZIH machines, please contact [Dr. Ulf
Markwardt](http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/wir_ueber_uns/mitarbeiter/markwardt).
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