Information Technology Reference
In-Depth Information
tutorials on how to construct and submit a job, and special simple workflows are
ready to use. For experienced users, more complex workflows are available or can
be assembled.
In the case of simple workflows, the user is relieved from most of the technical
details of the applied code. For both codes, computing jobs are typically driven by a
single input
file is uncomfortable for scientists to work with and it is
inflexible in the represented structure, e.g., blank lines at certain positions are
required. The required
file. This input
file is generated with the help of an adapter from the user
input to textboxes and list boxes with reasonable default values, taking advantage of
MSML. Machine-speci
c parameters, such as the number of cores, the wall time,
and the required memory are accessible through input
fields. For the convenience of
the users, they are preset to reasonable default values. A single listbox is populated
from an MSML dictionary entry containing frequently used combinations with the
Pople basis set 6-31G as the default. With respect to the needs of less experienced
users, the corresponding textbox supports an easily understandable four-column
data format. When the workflow is submitted, an adapter generates the necessary
input
file. Once successfully calculated, the geometry optimization is followed by
several post-processing steps.
More experienced users mostly prefer the expert workflow. Here an input
le
that was previously prepared by the user may be submitted directly. The true
strength of workflows can be utilized here when metaworkflows and parameter
sweep workflows are executed. Here, the advanced user can import workflows from
the SHIWA repository or the MoSGrid repository, or build them in the workflow
portlet.
11.4.2 Molecular Dynamics
In order to study larger molecular systems such as proteins and other biomolecules,
more ef
cient sampling methods have to be used. Therefore molecular dynamics
(MD) is employed, simplifying atomic interactions such as chemical bonds to e.g.,
harmonic potentials. This simpli
cation allows for simulation lengths of up to a
microsecond time scale, making biological events observable. The interactions
within a molecular system are described by the so-called force
field, that is, col-
lections of parameters for all kinds of atom types. Independent of the particular
selected force
field, all MD simulations follow in principle a similar workflow, which
can be considered as good simulation practice in the
field. First the molecule(s) of
interest need to be parameterized, or in other words, a topology based on a speci
c
force
field is generated. A periodic boundary box is then created around the system.
In order to mimic a nature-like environment solvent, ions are added to the box. Prior
to a longer production run, the molecular system needs to be minimized and equil-
ibrated. This is usually done over a multistep process using position constraints,
which are reduced from step to step.
Search WWH ::
Custom Search