CHARMM c24 mts.doc



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              ****************************************
              *   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 method.

*Menu:

* 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



File: MTS ]-[ Node: Syntax
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        ****************************************************
        * 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  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.
       [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.
       [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, no selected forces are
considered as long time scaled degree of freedom



File: MTS ]-[ Node: Desc
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            *******************************************
            *   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
CHARMM force field allow us to separate some time scales. But in gener
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 method is now only interact with the velocity Verlet algorithm.
   
c. Energy and forces from Urey-Bradely term is incoporated with bond
   command.

d. MTS method is interacted with Nose-Hoover mothod. In order to call Nose-
   Hoover method, you have to use Nose-Hoover module; see (nose.doc)
   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 have to specify SHAKE before calling
   MTS command. Only single reversible RESPA can be used with SHAKE.

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 (nbonds.doc)

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



File: MTS ]-[ Node: Note
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          ***********************************************
         * Energy routine and selections of MTS method *
          ***********************************************

Selections of MTS method depend on energy routines and nonbond
options. Followings are lists of possible selections.


1) GROUP selection
------------------
   Only single reversible RESPA method can be worked.
   Scalar include fast and slow routine.

   X - acceptable selection
   ------------------------------------------
   Selection | Vector   |  Scalar |  SHAKE
   ------------------------------------------
    BOND     |    X     |    X    |    X
    ANGL     |    X     |    X    |    X
    DIHE     |    X     |    X    |    X
    ALL      |    X     |    X    |    X
   ------------------------------------------
    MASS selection dosen't work with GROUP option.


2) ATOM selection 
-------------------
   S - Single reversible RESPA method
   D - Double reverisble RESPA method
   SHAKE only works with a single reversible RESPA method.

   X - acceptable selection
   ------------------------------------------
   Selection | Vector    |  Scalar   | SHAKE
             |  S  |  D  |  S  |  D  |   S
   ------------------------------------------
    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     |  X  |  X  |  X  |  X  |
   ------------------------------------------



File: MTS ]-[ Node: Exam
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              **************************************
              *    Examples of using MTS 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

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 

STOP

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