# mts (c37b1)

****************************************

* Multiple Time Scales Method (MTS) *

****************************************

In CHARMM, multiple time scales method (MTS) algorithm is similar

to code of the algorithm described in the paper by Tuckerman, Berne,

and Martyna [J.C.P., 97, 1990 (1992)]. Please refer to this paper for

details of derivations of this MTS-RESPA method. In addtion, more details

can be seen in J. Chem. Phys. 99, 8063 (1993) and J. Phys. Chem., 99, 5680

(1995) by M. Watanabe and M. Karplus. In this new release, MTS method can

be called under parallel platforms. All modules under MTS should work in

parallel. To run CHARMM in parallel, please refer to parallel.doc.

The MTS method can be combined with Langevin dynamics via the

LN algorithm, described by Barth and Schlick [J.Chem.Phys., 1998, in press].

This version includes the slow forces via extrapolation and is expected to

allow larger timesteps than reversible MTS-RESPA. See

general notes at the end of this documentation file.

LN algorithm was implemented in CHARMM by Eric Barth (8/97) and

Adrian Sandu (7/98).

In this documentation we refer to the rRESPA code as MTS-RESPA

(performing Newtonian dynamics) and to the LN code as MTS-LN

(performing Langevin dynamics).

* Syntax | Syntax of the MTS dynamics command

* Desc | Description of the keywords and options

* Note | Energy routines and MTS method selections

* Exam | Example of Multiple Time Scale Method

* Multiple Time Scales Method (MTS) *

****************************************

In CHARMM, multiple time scales method (MTS) algorithm is similar

to code of the algorithm described in the paper by Tuckerman, Berne,

and Martyna [J.C.P., 97, 1990 (1992)]. Please refer to this paper for

details of derivations of this MTS-RESPA method. In addtion, more details

can be seen in J. Chem. Phys. 99, 8063 (1993) and J. Phys. Chem., 99, 5680

(1995) by M. Watanabe and M. Karplus. In this new release, MTS method can

be called under parallel platforms. All modules under MTS should work in

parallel. To run CHARMM in parallel, please refer to parallel.doc.

The MTS method can be combined with Langevin dynamics via the

LN algorithm, described by Barth and Schlick [J.Chem.Phys., 1998, in press].

This version includes the slow forces via extrapolation and is expected to

allow larger timesteps than reversible MTS-RESPA. See

general notes at the end of this documentation file.

LN algorithm was implemented in CHARMM by Eric Barth (8/97) and

Adrian Sandu (7/98).

In this documentation we refer to the rRESPA code as MTS-RESPA

(performing Newtonian dynamics) and to the LN code as MTS-LN

(performing Langevin dynamics).

* Syntax | Syntax of the MTS dynamics command

* Desc | Description of the keywords and options

* Note | Energy routines and MTS method selections

* Exam | Example of Multiple Time Scale Method

Top

****************************************************

* Syntax for the Multiple Time Scaled Method (MTS) *

****************************************************

In this Multiple Time scaled method in CHARMM, a reversible RESPA

(Reference System Propagator Algorithm) is modified. (See Tuckerman's

paper about a reversible RESPA.) Two types of reversible RESPA methods

can be used in CHARMM.

1) Single reversible RESPA (Two-time-scale propagator)

MTSmethod 1 I

mts-spec

END

I :: multiple time scales (Integer) - See Description

mts-spec:: selection of hard forces or fast time scaled force

[BOND] ! Forces from all Bond-stretching motions

[ANGL] ! Forces from all angle-bending motions

[DIHE] ! Forces from all diheral motions and all improper

! torsional motion

[ALL ] ! Forces from all internal motions which are

! defined in CHAMM force fields

[MASS] 1 M ! Nonbonded forces involving atoms whose masses are

! less than M. M is a mass weight.

[SLFG] ! Nonbonded forces separation by long- and short-

! range forces (see more detail in the text)

[CLEA] ! Clear MTS module and assignments

2) Double reversible RESPA (Three-time-scale propagator)

MTSmethod I J

mts-spec

END

I and J :: multiple time scales (Integers) - See Description

mts-spec:: selections of fast and medium time scaled forces

[BOND] K ! Forces from all Bond-stretching motions

[ANGL] K ! Forces from all angle-bending motions

[DIHE] K ! Forces from all diheral motions and all improper

! torsional motion

[ALL ] K ! Forces from all internal motions which are

! defined in CHAMM force fields

[MASS] K M ! Nonbonded forces involving atoms whose masses are

! less than M. M is a mass weight.

[SLFG] ! Nonbonded forces separation by long- and short-

! range forces (see more detail in the text)

[CLEA] ! Clear MTS module and assignments

K is 1 or 2 - 1 - force considered as a short time scaled

2 - force considered as a medium time scaled

In both single and double RESPA methods, all interaciton forces, which

are not selected by MTS command, are considered as a long time scaled

degree of freedom

You can see the more details in J. Chem. Phys. 99, 8063 (1993) and

J. Phys. Chem., 99, 5680 (1995) by M. Watanabe and M. Karplus.

3) MASS (Atomic Mass force separation)

If MASS is selected, separating mass should be given.

MTS

.

.

MASS K M

END

K is the force considered as a short or medium time scaled. This

should be 1 or 2 ( 1 for short and 2 for medium )

M is the atomic mass. Separate the force contributions by the atomic

mass. Contributions from the atom less than M mass is considered as the

faster time scaled motions than those from the atom more than M mass.

See the more details about this in J. Phys. Chem. 99, 5680 (1995),

by M. Watanabe and M. Karplus.

4) SLFG (Short-Long Range force separation)

If SLFG is selected, Short range force cutoff distance (RSCUT),

switching function healing length (RHEA), and Buffer healing

length (BUFF) should be given by the following way:

MTS

.

SLFG RSCUT [number (6.0)] RHEA [number (1.0)] BUFF [number (1.0)]

END

[number] is the distance in the unit of Angstrom.

(..) is the default values.

See the more details about these lengths in J. Phys. Chem. 98, 6885,

(1994) by D.D.Humphreys, R.A.Friesner, and B.J. Berne.

****************************************************

* Syntax for the Multiple Time Scaled Method (MTS) *

****************************************************

In this Multiple Time scaled method in CHARMM, a reversible RESPA

(Reference System Propagator Algorithm) is modified. (See Tuckerman's

paper about a reversible RESPA.) Two types of reversible RESPA methods

can be used in CHARMM.

1) Single reversible RESPA (Two-time-scale propagator)

MTSmethod 1 I

mts-spec

END

I :: multiple time scales (Integer) - See Description

mts-spec:: selection of hard forces or fast time scaled force

[BOND] ! Forces from all Bond-stretching motions

[ANGL] ! Forces from all angle-bending motions

[DIHE] ! Forces from all diheral motions and all improper

! torsional motion

[ALL ] ! Forces from all internal motions which are

! defined in CHAMM force fields

[MASS] 1 M ! Nonbonded forces involving atoms whose masses are

! less than M. M is a mass weight.

[SLFG] ! Nonbonded forces separation by long- and short-

! range forces (see more detail in the text)

[CLEA] ! Clear MTS module and assignments

2) Double reversible RESPA (Three-time-scale propagator)

MTSmethod I J

mts-spec

END

I and J :: multiple time scales (Integers) - See Description

mts-spec:: selections of fast and medium time scaled forces

[BOND] K ! Forces from all Bond-stretching motions

[ANGL] K ! Forces from all angle-bending motions

[DIHE] K ! Forces from all diheral motions and all improper

! torsional motion

[ALL ] K ! Forces from all internal motions which are

! defined in CHAMM force fields

[MASS] K M ! Nonbonded forces involving atoms whose masses are

! less than M. M is a mass weight.

[SLFG] ! Nonbonded forces separation by long- and short-

! range forces (see more detail in the text)

[CLEA] ! Clear MTS module and assignments

K is 1 or 2 - 1 - force considered as a short time scaled

2 - force considered as a medium time scaled

In both single and double RESPA methods, all interaciton forces, which

are not selected by MTS command, are considered as a long time scaled

degree of freedom

You can see the more details in J. Chem. Phys. 99, 8063 (1993) and

J. Phys. Chem., 99, 5680 (1995) by M. Watanabe and M. Karplus.

3) MASS (Atomic Mass force separation)

If MASS is selected, separating mass should be given.

MTS

.

.

MASS K M

END

K is the force considered as a short or medium time scaled. This

should be 1 or 2 ( 1 for short and 2 for medium )

M is the atomic mass. Separate the force contributions by the atomic

mass. Contributions from the atom less than M mass is considered as the

faster time scaled motions than those from the atom more than M mass.

See the more details about this in J. Phys. Chem. 99, 5680 (1995),

by M. Watanabe and M. Karplus.

4) SLFG (Short-Long Range force separation)

If SLFG is selected, Short range force cutoff distance (RSCUT),

switching function healing length (RHEA), and Buffer healing

length (BUFF) should be given by the following way:

MTS

.

SLFG RSCUT [number (6.0)] RHEA [number (1.0)] BUFF [number (1.0)]

END

[number] is the distance in the unit of Angstrom.

(..) is the default values.

See the more details about these lengths in J. Phys. Chem. 98, 6885,

(1994) by D.D.Humphreys, R.A.Friesner, and B.J. Berne.

Top

*******************************************

* Description of MTS Dynamics Commands *

*******************************************

MTS method approach is effective for special system where a separation

between the fast and slow time components is natural. The nature of

there will be coupling between those motions, so this leads the

limitation of time scales.

a. In Multiple time scale, I and J are the number of cycle that you

want to calculate short time scaled and medium time scaled motions,

respectively, before calculating long time scaled motion.

Delta t = J * Dtau2 = I * J * Dtau1

where Dtau1 and Dtau1 are the integral time step for short and

medium time scaled motions respectively and Delta t is the integration

time step of long time scaled motions. Dtau1 is defined in DYNAmic

module as TIME.

b. MTS-RESPA method uses the velocity Verlet algorithm.

MTS-LN algorithm solves the simple Langevin equation and

relies on position Verlet and on constant extrapolation.

For MTS-RESPA (Newtonian dynamics) use "DYNA VVER ..."

For MTS-LN (Langevin dynamics) define FBETA and use "DYNA LNX ..."

c. Energy and forces from Urey-Bradely term is incoporated with bond

command.

d. MTS-RESPA method is interacted with Nose-Hoover method.

In order to call Nose-

Hoover method, you have to use Nose-Hoover module (» nose and

testcase for MTS method.)

e. If you are using with SHAKE, i.e. treat water molecules by SHAKE and

other molecules without SHAKE, you MUST specify SHAKE BEFORE calling

MTS command.

f. If you are going to use IMAGE module, you also have to specify the

module before calling MTS module.

g. MASS selection only works with ATOM nonbonded selection. (See

nonbond.doc)

h. all NONBOND and UPDATE options listed before calling MTS module

are highly recommended.

i. If SLFG selection is used, update frequency of nonbond list may be

specifically assgined in order to achieve the better energy

conservation of the system instead of using the automatic update

frequency (INBFRQ -1).

j. ENERGY module has to be called before calling MTS or after calling

dynamics. Otherwise, ENERGY cannot be calculated.

*******************************************

* Description of MTS Dynamics Commands *

*******************************************

MTS method approach is effective for special system where a separation

between the fast and slow time components is natural. The nature of

there will be coupling between those motions, so this leads the

limitation of time scales.

a. In Multiple time scale, I and J are the number of cycle that you

want to calculate short time scaled and medium time scaled motions,

respectively, before calculating long time scaled motion.

Delta t = J * Dtau2 = I * J * Dtau1

where Dtau1 and Dtau1 are the integral time step for short and

medium time scaled motions respectively and Delta t is the integration

time step of long time scaled motions. Dtau1 is defined in DYNAmic

module as TIME.

b. MTS-RESPA method uses the velocity Verlet algorithm.

MTS-LN algorithm solves the simple Langevin equation and

relies on position Verlet and on constant extrapolation.

For MTS-RESPA (Newtonian dynamics) use "DYNA VVER ..."

For MTS-LN (Langevin dynamics) define FBETA and use "DYNA LNX ..."

c. Energy and forces from Urey-Bradely term is incoporated with bond

command.

d. MTS-RESPA method is interacted with Nose-Hoover method.

In order to call Nose-

Hoover method, you have to use Nose-Hoover module (» nose and

testcase for MTS method.)

e. If you are using with SHAKE, i.e. treat water molecules by SHAKE and

other molecules without SHAKE, you MUST specify SHAKE BEFORE calling

MTS command.

f. If you are going to use IMAGE module, you also have to specify the

module before calling MTS module.

g. MASS selection only works with ATOM nonbonded selection. (See

nonbond.doc)

h. all NONBOND and UPDATE options listed before calling MTS module

are highly recommended.

i. If SLFG selection is used, update frequency of nonbond list may be

specifically assgined in order to achieve the better energy

conservation of the system instead of using the automatic update

frequency (INBFRQ -1).

j. ENERGY module has to be called before calling MTS or after calling

dynamics. Otherwise, ENERGY cannot be calculated.

Top

***********************************************

* Energy routine and selections of MTS method *

***********************************************

Selections of MTS method depend on energy routines and nonbond

options. Followings are lists of possible selections. (In the lists,

SHAKE means whether SHAKE method can be applied to the only enviroment,

such as water molecules.)

1) GROUP selection

------------------

S - Single reversible RESPA method

D - Double reverisble RESPA method

Scalar include fast and slow routine.

(SLFG only works with fast scalar routine.)

X - acceptable selection

----------------------------------------------

Selection | Vector | Scalar | SHAKE

| S | D | S | D | S | D

----------------------------------------------

BOND | X | | X | X | X | X

ANGL | X | | X | X | X | X

DIHE | X | | X | X | X | X

ALL | X | | X | X | X | X

MASS | | | | | |

SLFG | | | X | X | X | X

----------------------------------------------

MASS selection dosen't work with GROUP option.

2) ATOM selection

-------------------

S - Single reversible RESPA method

D - Double reverisble RESPA method

X - acceptable selection

----------------------------------------------

Selection | Vector | Scalar | SHAKE

| S | D | S | D | S | D

----------------------------------------------

BOND | X | X | X | X | X | X

ANGL | X | X | X | X | X | X

DIHE | X | X | X | X | X | X

ALL | X | X | X | X | X | X

MASS | X | X | X | X | |

SLFG | | | X | X | X | X

----------------------------------------------

***********************************************

* Energy routine and selections of MTS method *

***********************************************

Selections of MTS method depend on energy routines and nonbond

options. Followings are lists of possible selections. (In the lists,

SHAKE means whether SHAKE method can be applied to the only enviroment,

such as water molecules.)

1) GROUP selection

------------------

S - Single reversible RESPA method

D - Double reverisble RESPA method

Scalar include fast and slow routine.

(SLFG only works with fast scalar routine.)

X - acceptable selection

----------------------------------------------

Selection | Vector | Scalar | SHAKE

| S | D | S | D | S | D

----------------------------------------------

BOND | X | | X | X | X | X

ANGL | X | | X | X | X | X

DIHE | X | | X | X | X | X

ALL | X | | X | X | X | X

MASS | | | | | |

SLFG | | | X | X | X | X

----------------------------------------------

MASS selection dosen't work with GROUP option.

2) ATOM selection

-------------------

S - Single reversible RESPA method

D - Double reverisble RESPA method

X - acceptable selection

----------------------------------------------

Selection | Vector | Scalar | SHAKE

| S | D | S | D | S | D

----------------------------------------------

BOND | X | X | X | X | X | X

ANGL | X | X | X | X | X | X

DIHE | X | X | X | X | X | X

ALL | X | X | X | X | X | X

MASS | X | X | X | X | |

SLFG | | | X | X | X | X

----------------------------------------------

Top

********************************************

* Examples of using MTS-RESPA method *

********************************************

The followings are examples of MTS method. Also you can check two

testcases for MTS method.

! Multiple Time Scaled Method Start

! Part I - Single Reversible RESPA method

MTS 6 ! Integration time steps of 0.5fs for short time scale motions

! and 3.0fs for long time scales are used.

BOND ! Forces from all bond-stretching and bond bending motions

ANGL ! are treated as hard forces or short time scale degree of

! freedom

END

DYNA VVER STRT NSTEP 1000 TIME 0.0005 -

NPRINT 100 IPRFRQ 1000 -

INBFRQ 20 IHBFRQ 0 FIRSTT 200.0 -

IUNREA -30 IUNWRI 31 IUNCRD -32 IUNVEL -33 -

KUNIT -34 IUNO -41 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000

! Part II

! Double Reversible RESPA method

! Mass-scaling selection

MTS 5 2 ! Integration time steps -

! 0.5fs for short time scale motions

! 2.5fs for medium time scale motions and

! 5.0fs for long time scale motions

MASS 2 3.0 ! Nonbonded forces acting on atoms whose mass is less

! than 3.0g are treated as medium time scale.

BOND 1 ! Forces from all bond-stretching and angle-bending

ANGL 1 ! motions are considered as short time scale motions

DIHE 2 ! Forces from all dihedral and imporper torsion motions

! are considered as medium time scale.

END ! Rest of force contributions are considered as long time

! scaled motions

DYNA VVER REST NSTEP 1000 TIME 0.0005 -

NPRINT 100 IPRFRQ 1000 -

INBFRQ 20 IHBFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD -32 IUNVEL -33 -

KUNIT -34 IUNO -41 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000

! PartIII

! Short-long range selection of MTS

MTS 2 3 ! Integrated time step

! 0.5fs for the fast time scale

! 1.0fs for the medium time scale

! 3.0fs for the slow time scale

BOND 1 ! Forces from all bond-streching and angle-bending

ANGLE 1 ! motions are consideered as fast time scale motions

DIHE 2 ! Forces from all dihedral and improper torsion motions

! are considered as medium time scale

SLFG RSCUT 6.0 RHEA 2.0 BUFF 1.0

! Short-long range forces selection

! Short range forces are cut-off at 6.0A

END

DYNA VVER STRT NSTEP 200 TIME 0.0005 -

NPRINT 10 IPRFRQ 1000 -

FIRSTT 300.0 IUNREA -30 IUNWRI -31 IUNCRD -1 IUNVEL -1 -

KUNIT -1 IUNO -1 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000 -

TSTRUC 300

STOP

********************************************

* Examples of using MTS-RESPA method *

********************************************

The followings are examples of MTS method. Also you can check two

testcases for MTS method.

! Multiple Time Scaled Method Start

! Part I - Single Reversible RESPA method

MTS 6 ! Integration time steps of 0.5fs for short time scale motions

! and 3.0fs for long time scales are used.

BOND ! Forces from all bond-stretching and bond bending motions

ANGL ! are treated as hard forces or short time scale degree of

! freedom

END

DYNA VVER STRT NSTEP 1000 TIME 0.0005 -

NPRINT 100 IPRFRQ 1000 -

INBFRQ 20 IHBFRQ 0 FIRSTT 200.0 -

IUNREA -30 IUNWRI 31 IUNCRD -32 IUNVEL -33 -

KUNIT -34 IUNO -41 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000

! Part II

! Double Reversible RESPA method

! Mass-scaling selection

MTS 5 2 ! Integration time steps -

! 0.5fs for short time scale motions

! 2.5fs for medium time scale motions and

! 5.0fs for long time scale motions

MASS 2 3.0 ! Nonbonded forces acting on atoms whose mass is less

! than 3.0g are treated as medium time scale.

BOND 1 ! Forces from all bond-stretching and angle-bending

ANGL 1 ! motions are considered as short time scale motions

DIHE 2 ! Forces from all dihedral and imporper torsion motions

! are considered as medium time scale.

END ! Rest of force contributions are considered as long time

! scaled motions

DYNA VVER REST NSTEP 1000 TIME 0.0005 -

NPRINT 100 IPRFRQ 1000 -

INBFRQ 20 IHBFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD -32 IUNVEL -33 -

KUNIT -34 IUNO -41 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000

! PartIII

! Short-long range selection of MTS

MTS 2 3 ! Integrated time step

! 0.5fs for the fast time scale

! 1.0fs for the medium time scale

! 3.0fs for the slow time scale

BOND 1 ! Forces from all bond-streching and angle-bending

ANGLE 1 ! motions are consideered as fast time scale motions

DIHE 2 ! Forces from all dihedral and improper torsion motions

! are considered as medium time scale

SLFG RSCUT 6.0 RHEA 2.0 BUFF 1.0

! Short-long range forces selection

! Short range forces are cut-off at 6.0A

END

DYNA VVER STRT NSTEP 200 TIME 0.0005 -

NPRINT 10 IPRFRQ 1000 -

FIRSTT 300.0 IUNREA -30 IUNWRI -31 IUNCRD -1 IUNVEL -1 -

KUNIT -1 IUNO -1 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000 -

TSTRUC 300

STOP

Top

*****************************************

* Examples of using MTS-LN method *

*****************************************

! PartIV

! LN algorithm - MTS with Langevin dynamics

!

! Langevin coupling parameter needs to be defined

SCALAR FBETA SET 20 SELE ALL END

! Shake, if needed

SHAKE BONH PARAM TOL 1.0D-9 SELE RESNAME TIP3 END

MTS 4 24 ! Integrated time step

! 0.5 fs for the fast timestep

! 2.0 fs for the medium timestep

! 48.0 fs for the slow timestep

BOND 1 ! Forces from all bond-streching and angle-bending

ANGLE 1 ! motions are consideered as fast time scale motions

DIHE 1 ! Forces from all dihedral and improper torsion motions

! are considered as medium time scale

SLFG RSCUT 6.0 RHEA 2.0 BUFF 1.0

! Distance class definition

! Short range forces are cut-off at 6.0A

END

DYNA LNX STRT NSTEP 200 TIME 0.0005 -

NPRINT 10 IPRFRQ 1000 -

FIRSTT 300.0 IUNREA -30 IUNWRI -31 IUNCRD -1 IUNVEL -1 -

KUNIT -1 IUNO -1 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000 -

TSTRUC 300

STOP

*****************************************

* Examples of using MTS-LN method *

*****************************************

! PartIV

! LN algorithm - MTS with Langevin dynamics

!

! Langevin coupling parameter needs to be defined

SCALAR FBETA SET 20 SELE ALL END

! Shake, if needed

SHAKE BONH PARAM TOL 1.0D-9 SELE RESNAME TIP3 END

MTS 4 24 ! Integrated time step

! 0.5 fs for the fast timestep

! 2.0 fs for the medium timestep

! 48.0 fs for the slow timestep

BOND 1 ! Forces from all bond-streching and angle-bending

ANGLE 1 ! motions are consideered as fast time scale motions

DIHE 1 ! Forces from all dihedral and improper torsion motions

! are considered as medium time scale

SLFG RSCUT 6.0 RHEA 2.0 BUFF 1.0

! Distance class definition

! Short range forces are cut-off at 6.0A

END

DYNA LNX STRT NSTEP 200 TIME 0.0005 -

NPRINT 10 IPRFRQ 1000 -

FIRSTT 300.0 IUNREA -30 IUNWRI -31 IUNCRD -1 IUNVEL -1 -

KUNIT -1 IUNO -1 NSAVC 5 NSAVV 5 NSNOS 10 ISVFRQ 1000 -

TSTRUC 300

STOP

Top

**************************************

* Parameter settings for LN *

**************************************

The algorithm relies on existing CHARMM force splitting routines under

the MTS command. The LN slow forces are incorporated via extrapolation as

opposed to "impulses" as in the MTS-RESPA method. This alleviates severe

resonance problems and permits larger outer timesteps to be used for

additional speedup.

The LN algorithm is compatible with SHAKE and with the use of boundary

conditions. Any other combinations of options have not been tested.

There are several parameters that are set for a LN simulation:

1. Langevin parameter gamma (FBETA in CHARMM notation), the damping constant:

* Recommended value = 5 to 20 ps^(-1)

Too small a value will render the simulation unstable. On the other

hand, the larger gamma is, the greater the overdamping of the

low-frequency modes. The above recommendation reflects a balance

found by experimentation. Gamma can also be simulation-goal dependent.

2. Timestep Protocol for force splitting:

Dt(fast) = inner TIMESTEP for updating the "fast" forces

* Recommended value = 0.5 -- 1 fs (no shake)

1 -- 2 fs (with shake)

Dt(medium) = K1*Dt(fast), update frequency for "medium" forces

* Recommended value = 1 -- 3 fs

Dt(long) = K2*Dt(medium), update frequency for "slow" forces

* Recommended value = 6 -- 200 fs

Larger computational savings can be realized with a larger Dt(long).

However, the speedup is limited and reaches an asymptotic value

since the evaluation of medium forces becomes increasingly costly.

The asymptotic maximum speedup can be reached for outer timesteps of

24 or 48 fs, for example, but the precise value depends on the timestep

protocol employed and the application system. This should be tested

carefully by the user for the problem at hand.

3. Definition of the force splitting classes:

Recommended Protocol --:

* Fast forces = BOND 1, ANGL 1, DIHE 1

* Medium forces = Nonbond cutoff

cutoff distance = 6 A - 8 A

healing region = 1 A - 3 A

buffer region = 1 A - 3 A

SLFG RSCUT [cutoff distance] RHEA [healing region] BUFF [buffer region]

* Longrange forces = remaining terms

Nonboned pairlists are currently updated in the LN code

every outer timestep; it is possible (but more costly)

to attempt the updating every medium timestep.

The nonbonded pairlist is updated in the current

implementation every Dt(long).

4. The GROUP electrostatics option works much better

than ATOM electrostatics.

Use of the latter is discouraged based on our test problems.

*******************************************************************

PLEASE NOTE: All the LN parameters above can be sensitive to the

----------- specific protocol used for the dynamics simulations

and are problem dependent (see discussion of results

in the LN papers).

For further guidance, feel free to contact Tamar

Schlick at the email: schlick@nyu.edu

*******************************************************************

**************************************

* Parameter settings for LN *

**************************************

The algorithm relies on existing CHARMM force splitting routines under

the MTS command. The LN slow forces are incorporated via extrapolation as

opposed to "impulses" as in the MTS-RESPA method. This alleviates severe

resonance problems and permits larger outer timesteps to be used for

additional speedup.

The LN algorithm is compatible with SHAKE and with the use of boundary

conditions. Any other combinations of options have not been tested.

There are several parameters that are set for a LN simulation:

1. Langevin parameter gamma (FBETA in CHARMM notation), the damping constant:

* Recommended value = 5 to 20 ps^(-1)

Too small a value will render the simulation unstable. On the other

hand, the larger gamma is, the greater the overdamping of the

low-frequency modes. The above recommendation reflects a balance

found by experimentation. Gamma can also be simulation-goal dependent.

2. Timestep Protocol for force splitting:

Dt(fast) = inner TIMESTEP for updating the "fast" forces

* Recommended value = 0.5 -- 1 fs (no shake)

1 -- 2 fs (with shake)

Dt(medium) = K1*Dt(fast), update frequency for "medium" forces

* Recommended value = 1 -- 3 fs

Dt(long) = K2*Dt(medium), update frequency for "slow" forces

* Recommended value = 6 -- 200 fs

Larger computational savings can be realized with a larger Dt(long).

However, the speedup is limited and reaches an asymptotic value

since the evaluation of medium forces becomes increasingly costly.

The asymptotic maximum speedup can be reached for outer timesteps of

24 or 48 fs, for example, but the precise value depends on the timestep

protocol employed and the application system. This should be tested

carefully by the user for the problem at hand.

3. Definition of the force splitting classes:

Recommended Protocol --:

* Fast forces = BOND 1, ANGL 1, DIHE 1

* Medium forces = Nonbond cutoff

cutoff distance = 6 A - 8 A

healing region = 1 A - 3 A

buffer region = 1 A - 3 A

SLFG RSCUT [cutoff distance] RHEA [healing region] BUFF [buffer region]

* Longrange forces = remaining terms

Nonboned pairlists are currently updated in the LN code

every outer timestep; it is possible (but more costly)

to attempt the updating every medium timestep.

The nonbonded pairlist is updated in the current

implementation every Dt(long).

4. The GROUP electrostatics option works much better

than ATOM electrostatics.

Use of the latter is discouraged based on our test problems.

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PLEASE NOTE: All the LN parameters above can be sensitive to the

----------- specific protocol used for the dynamics simulations

and are problem dependent (see discussion of results

in the LN papers).

For further guidance, feel free to contact Tamar

Schlick at the email: schlick@nyu.edu

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