**************************************** * 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
**************************************************** * 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
******************************************* * 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.
*********************************************** * 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 | ------------------------------------------
************************************** * 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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FDA/CBER/OVRR Biophysics Laboratory