MTS_RESPA

NAME
MTS_RESPA - Use a multiple time step integrator

SYNOPSIS
MTS_RESPA
....
END

DESCRIPTION
The MTS_RESPA structured command opens an environment which includes several subcommands used to define a multiple time step integrator. The MTS_RESPA directive can be specified for NVE simulations and extended system simulations NHP, NPT and NVT. MTS_RESPA is also compatible with constraints. The following subcommands may be specified within MTS_RESPA:

step dirty very_cold_start energy_then_die k-ewald test-times p_test s_test

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step    type n    [r  [ hl  [dr]]]  [reciprocal]
The command step is used to define the potential subdivision and the corresponding time steps. The string type can be either ``intra'' or ``nonbond'': in the former case the command defines an intramolecular shell, whereas in the latter a nonbonded shell is defined. If ``intra'' is specified only one keyword is expected, i.e. the integer n. When two subcommand of the type - step intra n - are entered, the first is assumed to refer to the faster intramolecular subsystem (the $V_{n0}$ subsystem as defined in eq. 4.3 with $n = n0$) and the second is assumed to define the slower intramolecular subsystem (the $V_{n1}$ subsystem as defined in eq. 4.3 with $n=n1$). If only one subcommand - step intra n - is entered then $n0$ is set to 1 and and $n1=n$. If no - step intra n subcommand is given then $n1=n0=1$.

If the first argument of the step subcommand is the string ``nonbond'' then at least an integer and a real are expected. The integer $n$ is the time step dividing factor of the nonbonded shell while the real argument equals the shell upper radius. Two more optional real arguments can be defined, i.e. the healing length at the upper shell radius and the corresponding neighbor list offset. The defaults value of the healing length are As for the intra shell, the more rapidly varying nonbonded shells are entered first. If three - step nonbond - subcommands are entered, then the first refers to the $V_{m}$, the second to the $V_{l}$ and the third to the $V_{h}$ subsystems, with $n$ being $m,l,1$ such that $\Delta t_{h} = \Delta t$, $\Delta t_{l} = \Delta t_{h}/l$, $\Delta t_{m} = \Delta t_{l}/m$, (see Table 4.3). $n$ for the last nonbonded shell is set automatically to 1 disregarding its actual value. If two shells are entered then only two intermolecular time steps are used, i.e. $n=m$ and $l=1$. If one shell is entered only one time step is defined and $m=l=1$. When using Ewald, the $V_{qr}$ term (Eq. 4.21) in the reciprocal lattice is assigned by entering the string reciprocal as the last argument of a - step nonbond directive.

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k-ewald kl   lambdakl   km   lambdakm - Obsolete - Unsupported
$kl$ and $km$ define the shells in reciprocal space. Wave vectors $k=\vert{\bf k}\vert$ such that $rkcut \ge k > kl$, $kl \ge k > km$, and $km \ge k > 0$ are assigned to the $h$-shell $l$-shell and $m$-shell, respectively. lambdakm, lambdakl are the upper healing lengths for the reciprocal space $m$ and $l$ shells and the lower healing length for the reciprocal space $h$ and $l$ shells, respectively.
Warning: To be used only when on is specified in the directive EWALD (environment &POTENTIAL); $rkcut$ must be defined in the directive EWALD). The reciprocal lattice assignment is best done via the keyword reciprocal of the command step nonbond.

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test-times OPEN $filename$ - Diagnostic - Unsupported
Produce the time record of the potential and kinetic energies at the end of the propagation step (i.e. at intervals of $\Delta t_{h}~ fs$). The following is the format used for dumping the energies:

      WRITE(ktest,300) tim,utot,ustot,uptot,upstot,ektot,pottot
300   FORMAT(' TotalEnergy',f12.3,6f15.3)

Where tim,utot,ustot,uptot,upstot,ektot,pottot are the values of the time, total energy, solvent potential energy, solute potential energy, solvent-solute potential energy, total kinetic energy, total potential energy. Time is given in fs and all energies in $KJ/mole$. The energy conservation ratio $R \equiv \Delta E / \Delta K$ and the drift $D = {(E - \langle E \rangle)t \over t(t-\langle t \rangle )}$ are printed periodically (every $1000*\Delta t_{h}$) and at the end of the simulation onto the file $filename$.

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dirty - Obsolete - Unsupported
Scales velocities to the initial total energy $E(0)$ during production stage. The scaling is done randomly with a Monte Carlo algorithm.

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p_test $n1$ $n2$ $n3$ $n4$ $n5$ - Diagnostic - Unsupported
To be used in conjunction with subcommand test-times: print out time record of the subsystems potential and forces for the protein for atoms $n1$ $n2$ $n3$ $n4$ $n5$.

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s_test $n1$ $n2$ $n3$ - Diagnostic - Unsupported
To be used in conjunction with subcommand test-times: print out time record of the subsystems potential and forces for the solvent for atoms $n1$ $n2$ $n3$.

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very_cold_start rmax
This option is useful when minimizing a protein in a highly unfavorable configuration. The real argument $rmax$ is the maximum allowed displacement (in Å) for any atom when integrating the equations of motion irrespective of the intensity of the force on that atom. This constraint avoid blowing up of the simulation.

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energy_then_die
Print out energies and then stops.

EXAMPLES

 
 step intra 2  
 step intra 2
 step nonbond 4 4.2  
 step nonbond 4 7.3  reciprocal   
 step nonbond 1 9.7

Here five time steps are defined, three for nonbonded potentials and two for intramolecular potential. The largest timestep $\Delta t_{h}$ is defined by the command TIMESTEP in this environment (see above) and refers to the nonbonded subsystem with shell in the range $7.3-9.7$ Å. We then have $\Delta t_{l} = \Delta t_{h}/4$ referring to the $4.2-7.3$ Å shell and $\Delta t_{l} = \Delta t_{h}/4/4$ referring to the $0-4.2$ Å shell. The reciprocal potential is assigned to the intermediate $4.2-7.3$ Å shell. The two intramolecular shells have time steps $\Delta t_{n1} = \Delta t_{h}/4/4/2$ and $\Delta t_{n0} = \Delta t_{h}/4/4/2/2$.

 
 step intra 2  
 step nonbond 3 6.5  reciprocal
 step nonbond 1 9.5  
 test-times OPEN file-tests

Here only one intramolecular and two intermolecular time steps are defined. The reciprocal (PME or standard) contribution is assigned to the fastest intermolecular shell. Energy records are printed onto the file file-tests each $\Delta t_{h}$ femtoseconds.

DEFAULTS

 step intra 1  
 step intra 1
 step nonbond 1 4.1 0.3 0.35 
 step nonbond 1 7.3 0.3 0.45  reciprocal   
 step nonbond 1 9.7 0.3 1.5

WARNINGS

1

When standard Ewald is used and the reciprocal space contribution is subdivided in k-shells, the intramolecular term of Eq. 4.21 is always assigned to the fastest k-shell. This may cause instability of the integration. Subdivision of the reciprocal lattice contribution with standard Ewald, although technically possible, is not recommended.

2

The directive dirty makes fast integrators stable but may severely affect dynamical properties.