| 498 |
|
{\tt minimizer} & string & Chooses a minimizer & Possible minimizers |
| 499 |
|
are SD and CG. Either {\tt ensemble} or {\tt minimizer} must be specified. \\ |
| 500 |
|
{\tt ensemble} & string & Sets the ensemble. & Possible ensembles are |
| 501 |
< |
NVE, NVT, NPTi, NPAT, NPTf, and NPTxyz. Either {\tt ensemble} |
| 501 |
> |
NVE, NVT, NPTi, NPAT, NPTf, NPTxyz, and LD. Either {\tt ensemble} |
| 502 |
|
or {\tt minimizer} must be specified. \\ |
| 503 |
|
{\tt dt} & fs & Sets the time step. & Selection of {\tt dt} should be |
| 504 |
|
small enough to sample the fastest motion of the simulation. ({\tt |
| 1905 |
|
& (with changes to box shape) & \\ |
| 1906 |
|
NPTxyz & approximate isobaric-isothermal & {\tt ensemble = NPTxyz;} \\ |
| 1907 |
|
& (with separate barostats on each box dimension) & \\ |
| 1908 |
+ |
LD & Langevin Dynamics & {\tt ensemble = LD;} \\ |
| 1909 |
+ |
& (approximates the effects of an implicit solvent) & \\ |
| 1910 |
|
\end{tabular} |
| 1911 |
|
\end{center} |
| 1912 |
|
|
| 2372 |
|
orientational anisotropy in the system (i.e. in lipid bilayer |
| 2373 |
|
simulations). |
| 2374 |
|
|
| 2375 |
< |
\section{Langevin Dynamics (LANGEVINDYNAMICS)\label{LDRB}} |
| 2375 |
> |
\section{Langevin Dynamics (LD)\label{LDRB}} |
| 2376 |
|
|
| 2377 |
< |
{\sc oopse} implements a Langevin dynamics integrator in order to |
| 2378 |
< |
perform molecular dynamics simulations in implicit solvent |
| 2379 |
< |
environments. This results in substantial performance gains when the |
| 2380 |
< |
detailed dynamics of the solvent is not important. Since {\sc oopse} |
| 2381 |
< |
also handles rigid bodies of arbitrary composition and shape, the |
| 2382 |
< |
Langevin integrator is somewhat more complex than in other simulation |
| 2381 |
< |
packages. |
| 2377 |
> |
{\sc oopse} implements a Langevin integrator in order to perform |
| 2378 |
> |
molecular dynamics simulations in implicit solvent environments. This |
| 2379 |
> |
can result in substantial performance gains when the detailed dynamics |
| 2380 |
> |
of the solvent is not important. Since {\sc oopse} also handles rigid |
| 2381 |
> |
bodies of arbitrary composition and shape, the Langevin integrator is |
| 2382 |
> |
by necessity somewhat more complex than in other simulation packages. |
| 2383 |
|
|
| 2384 |
|
Consider the Langevin equations of motion in generalized coordinates |
| 2385 |
|
\begin{equation} |
| 2436 |
|
2 k_B T \Xi_R \delta(t - t'). \label{eq:randomForce} |
| 2437 |
|
\end{equation} |
| 2438 |
|
$\Xi_R$ is the $6\times6$ resistance tensor at the center of |
| 2439 |
< |
resistance. Once this tensor is known for a given rigid body (as |
| 2440 |
< |
described in the previous section) obtaining a stochastic vector that |
| 2441 |
< |
has the properties in Eq. (\ref{eq:randomForce}) can be done |
| 2442 |
< |
efficiently by carrying out a one-time Cholesky decomposition to |
| 2443 |
< |
obtain the square root matrix of the resistance tensor, |
| 2439 |
> |
resistance. |
| 2440 |
> |
|
| 2441 |
> |
For atoms and ellipsoids, there are good approximations for this |
| 2442 |
> |
tensor that are based on Stokes' law. For arbitrary rigid bodies, the |
| 2443 |
> |
resistance tensor must be pre-computed before Langevin dynamics can be |
| 2444 |
> |
used. The {\sc oopse} distribution contains a utitilty program called |
| 2445 |
> |
Hydro that performs this computation. |
| 2446 |
> |
|
| 2447 |
> |
Once this tensor is known for a given {\tt integrableObject}, |
| 2448 |
> |
obtaining a stochastic vector that has the properties in |
| 2449 |
> |
Eq. (\ref{eq:randomForce}) can be done efficiently by carrying out a |
| 2450 |
> |
one-time Cholesky decomposition to obtain the square root matrix of |
| 2451 |
> |
the resistance tensor, |
| 2452 |
|
\begin{equation} |
| 2453 |
|
\Xi_R = {\bf S} {\bf S}^{T}, |
| 2454 |
|
\label{eq:Cholesky} |
| 2486 |
|
\begin{equation} |
| 2487 |
|
\frac{\partial}{\partial t}{\bf j}(t) = \tau^{~b}(t) |
| 2488 |
|
\end{equation} |
| 2489 |
< |
Embedding the friction and random forces into the the total force and |
| 2490 |
< |
torque, one can integrate the Langevin equations of motion for a rigid |
| 2491 |
< |
body of arbitrary shape in a velocity-Verlet style 2-part algorithm, |
| 2492 |
< |
where $h = \delta t$: |
| 2489 |
> |
By embedding the friction and random forces into the the total force |
| 2490 |
> |
and torque, {\sc oopse} integrates the Langevin equations of motion |
| 2491 |
> |
for a rigid body of arbitrary shape in a velocity-Verlet style 2-part |
| 2492 |
> |
algorithm, where $h = \delta t$: |
| 2493 |
|
|
| 2494 |
|
{\tt move A:} |
| 2495 |
|
\begin{align*} |
| 2594 |
|
+ \frac{h}{2} {\bf \tau}^{~b}(t + h) . |
| 2595 |
|
\end{align*} |
| 2596 |
|
|
| 2597 |
< |
The viscosity of the implicit of solvents must be specified using {\tt |
| 2598 |
< |
viscosity} keywords in the meta-data file to use langevin dynamics |
| 2599 |
< |
integrator. For simple shaped particles (spheres and ellipsoids), no |
| 2600 |
< |
further parameters are necessary. However, there are no analytical |
| 2601 |
< |
solutions for composite shaped particles, the approximate methods have |
| 2602 |
< |
to be applied to get the resistance tensor. The file which contains |
| 2603 |
< |
the information about hydro properties is indicated by {\tt |
| 2604 |
< |
HydroPropFile} keyword in meta-data file. The {\tt HydroPropFile} is |
| 2605 |
< |
precalculated by {\tt Hydro}. |
| 2606 |
< |
|
| 2607 |
< |
\begin{longtable}[c]{ABCD} |
| 2608 |
< |
\caption{Meta-data Keywords: Langevin Dynamics Parameters} |
| 2597 |
> |
The viscosity of the implicit solvent must be specified using the {\tt |
| 2598 |
> |
viscosity} keyword in the meta-data file if the Langevin integrator is |
| 2599 |
> |
selected. For simple particles (spheres and ellipsoids), no further |
| 2600 |
> |
parameters are necessary. Since there are no analytic solutions for |
| 2601 |
> |
the resistance tensors for composite rigid bodies, the approximate |
| 2602 |
> |
tensors for these objects must also be specified in order to use |
| 2603 |
> |
Langevin dynamics. The meta-data file must therefore point to another |
| 2604 |
> |
file which contains the information about the hydrodynamic properties |
| 2605 |
> |
of all complex rigid bodies being used during the simulation. The |
| 2606 |
> |
{\tt HydroPropFile} keyword is used to specify the name of this |
| 2607 |
> |
file. A {\tt HydroPropFile} should be precalculated using the Hydro |
| 2608 |
> |
program that is included in the {\sc oopse} distribution. |
| 2609 |
> |
|
| 2610 |
> |
\begin{longtable}[c]{ABG} |
| 2611 |
> |
\caption{Meta-data Keywords: Required parameters for the Langevin integrator} |
| 2612 |
|
\\ |
| 2613 |
< |
{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
| 2613 |
> |
{\bf keyword} & {\bf units} & {\bf use} \\ \hline |
| 2614 |
|
\endhead |
| 2615 |
|
\hline |
| 2616 |
|
\endfoot |
| 2617 |
< |
{\tt viscosity} & centipoise & Sets the value of viscosity of implicit |
| 2618 |
< |
solvents & \\ {\tt HydroPropFile} & string & specifies the resistance |
| 2619 |
< |
tensor file & usually a {\tt .diff} file which is precalculated by |
| 2620 |
< |
{\sc Hydro}. Not necessory for simple shaped particles (spheres and |
| 2621 |
< |
ellipsoids) \\ |
| 2622 |
< |
{\tt beadSize} & $\mbox{\AA}$ & Sets the diameters of |
| 2623 |
< |
beads when {\sc Rough Shell Model} is used to generate the resistance |
| 2624 |
< |
tensor file. \\ |
| 2617 |
> |
{\tt viscosity} & centipoise & Sets the value of viscosity of the implicit |
| 2618 |
> |
solvent \\ |
| 2619 |
> |
{\tt targetTemp} & K & Sets the target temperature of the system. |
| 2620 |
> |
This parameter must be specified to use Langevin dynamics. \\ |
| 2621 |
> |
{\tt HydroPropFile} & string & Specifies the name of the resistance |
| 2622 |
> |
tensor (usually a {\tt .diff} file) which is precalculated by {\tt |
| 2623 |
> |
Hydro}. This keyworkd is not necessary if the simulation contains only |
| 2624 |
> |
simple bodies (spheres and ellipsoids). \\ |
| 2625 |
> |
{\tt beadSize} & $\mbox{\AA}$ & Sets the diameter of the beads to use |
| 2626 |
> |
when the {\tt RoughShell} model is used to approximate the resistance |
| 2627 |
> |
tensor. |
| 2628 |
|
\label{table:ldParameters} |
| 2629 |
|
\end{longtable} |
| 2630 |
|
|
| 2616 |
– |
|
| 2631 |
|
\section{\label{sec:constraints}Constraint Methods} |
| 2632 |
|
|
| 2633 |
|
\subsection{\label{oopseSec:rattle}The {\sc rattle} Method for Bond |
| 3473 |
|
\end{longtable} |
| 3474 |
|
|
| 3475 |
|
\section{\label{oopseSec:Hydro}Hydro} |
| 3476 |
< |
{\tt Hydro} generates {\tt .diff} file which is required when a Langevin |
| 3477 |
< |
Dynamics simulation using approximate models (supports Bead Model and |
| 3478 |
< |
Rough Shell Model) is performed. To generate the {\tt }.diff file, the |
| 3479 |
< |
meta-data file is needed as the input file. The viscosity of the fluid |
| 3480 |
< |
flow (solvent) and the temperature of the system have to be defined in |
| 3481 |
< |
meta-data file. If the approximate model is {\tt Rough Shell Model}, |
| 3482 |
< |
the {\tt beadSize} which is the diameter of every beads must be |
| 3483 |
< |
specified in meta-data file. |
| 3476 |
> |
{\tt Hydro} generates resistance tensor ({\tt .diff}) files which are |
| 3477 |
> |
required when using the Langevin integrator using complex rigid |
| 3478 |
> |
bodies. {\tt Hydro} supports two approximate models: the {\tt |
| 3479 |
> |
BeadModel} and {\tt RoughShell}. Additionally, {\tt Hydro} can |
| 3480 |
> |
generate resistance tensor files using analytic solutions for simple |
| 3481 |
> |
shapes. To generate a {\tt }.diff file, a meta-data file is needed as |
| 3482 |
> |
the input file. Since the resistance tensor depends on these |
| 3483 |
> |
quantities, the {\tt viscosity} of the solvent and the temperature |
| 3484 |
> |
({\tt targetTemp}) of the system must be defined in meta-data file. If |
| 3485 |
> |
the approximate model in use is the {\tt RoughShell} model the {\tt |
| 3486 |
> |
beadSize} (the diameter of the small beads used to approximate the |
| 3487 |
> |
surface of the body) must also be specified. |
| 3488 |
|
|
| 3489 |
|
The options available for Hydro are as follows: |
| 3490 |
|
\begin{longtable}[c]{|EFG|} |
| 3498 |
|
-V& {\tt -{}-version} & Print version and exit\\ |
| 3499 |
|
-i& {\tt -{}-input=filename} & input MetaData (md) file\\ |
| 3500 |
|
-o& {\tt -{}-output=STRING} & Output file name\\ |
| 3501 |
< |
& {\tt -{}-model=STRING} & hydrodynamics model (supports |
| 3502 |
< |
RoughShell and BeadModel)\\ |
| 3501 |
> |
& {\tt -{}-model=STRING} & hydrodynamics model (supports both |
| 3502 |
> |
{\tt RoughShell} and {\tt BeadModel})\\ |
| 3503 |
|
-b& {\tt -{}-beads} & generate the beads only, |
| 3504 |
< |
hydrodynamics will be performed (default=off)\\ |
| 3504 |
> |
hydrodynamic calculations will not be performed (default=off)\\ |
| 3505 |
|
\end{longtable} |
| 3506 |
|
|
| 3507 |
|
|
