Self-Guided Langevin Dynamics (SGLD) simulation
By Xiongwu Wu and Bernard R. Brooks
The SGLD simulation is a Langevin/Molecular Dynamics simulation with
enhanced systematic motion. A guiding force which is a local average
of friction forces is calculated during the simulation and used to
enhance slow motions. This method is implemented in DYNAMC command and
can be activated by a "SGLD" or "SGMD" key word. For SGLD simulation,
friction constants need be defined. A similar algorithm is implemented
for MD simulation and is activated by the keyword "SGMD".
Two guiding parameters, local average time (TSGAVG) and guiding
factor (SGFT), are used to define the guiding effect as well as the
friction constants for Langevin dynamics. A larger TSGAVG will result in
slower motion to be enhanced. A larger SGFT will introduce stronger guiding
forces and results in larger energy barrier overcoming ability. To avoid the
difficulty in chosing the value of SGFT, a parameter called guiding
temperature (TEMPSG) is introduced. When TEMPSG is set larger than 0,
SGFT will be set constantly by CHARMM to make the guiding force
corresponding to a systematic motion at a temperature given by TEMPSG. User
can monitor the instant SGFT and TEMPSG in CHARMM output by setting PRNLEV>4.
A larger TEMPSG results in more enhancement in slow motion. If a constant
SGFT simulation is desired, one can first set TEMPSG=1K in a short simulation
to get an approximate value of SGFT.
* Menu:
* Syntax:: Syntax of the SGLD dynamics command
* Examples:: SGLD usage examples
[Syntax SGLD]
DYNAMC [SGLD] [SGMD] TSGAVG real [TEMPSG real|SGFT real] [SGMV] -
other-dynamc-spec
Keyword Default Purpose
SGLD false Turn on SGLD simulation (for Langevin dynamics)
SGMD false Turn on SGMD simulation (for MD simulations)
TSGAVG 0.5 ps Local average time
SGFT 0.5 Guiding factor
TEMPSG 0.0 K Guiding temperature. TEMPSG>0 will override SGFT.
SGMV false Allow guiding force on the center of mass
Examples
1) SGLD simulation with a friction constant of 1/ps.
! Set friction forces
SCAL FBETA SET 1.0 SELE ALL END
! Perform SGLD simulation
DYNA LANG LEAP STRT NSTE 1000000 TIME 0.002 -
IPRFRQ 10000 ISVFRQ 1000 IHTFRQ 0 IEQFRQ 0 INBFRQ 10 IHBFRQ 0 -
IUNREA -1 IUNWRI 31 IUNCRD 32 IUNVEL 33 KUNIT -1 -
NSAVC 1000 NSAVV 00 NPRINT 1000 ISEED 314159 -
SGLD TSGAVG 0.2 SGFT 0.5 -
TBATH 300 FIRST 260 -
IASORS 0 IASVEL 1 ICHECW 0 -
NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSWIT -
CUTNB 14.0 CTOFNB 13.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.0
2) SGLD simulation with a particle in external potential surface.
Guiding force on the center of mass is needed.
! Set friction forces
SCAL FBETA SET 1.0 SELE ALL END
! Perform SGLD simulation
DYNA LANG LEAP STRT NSTE 1000000 TIME 0.002 -
IPRFRQ 10000 ISVFRQ 1000 IHTFRQ 0 IEQFRQ 0 INBFRQ 10 IHBFRQ 0 -
IUNREA -1 IUNWRI 31 IUNCRD 32 IUNVEL 33 KUNIT -1 -
NSAVC 1000 NSAVV 00 NPRINT 1000 ISEED 314159 -
! Specify SGMV to allow guiding force on the center of mass
SGLD TSGAVG 0.5 SGFT 0.5 SGMV -
TBATH 300 FIRST 260 -
IASORS 0 IASVEL 1 ICHECW 0 -
NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSWIT -
CUTNB 14.0 CTOFNB 13.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.0
3) SGLD simulation with a constant guiding temperature of 1 K.
! Set friction forces
SCAL FBETA SET 1.0 SELE ALL END
! Perform SGLD simulation
DYNA LANG LEAP STRT NSTE 1000000 TIME 0.002 -
IPRFRQ 10000 ISVFRQ 1000 IHTFRQ 0 IEQFRQ 0 INBFRQ 10 IHBFRQ 0 -
IUNREA -1 IUNWRI 31 IUNCRD 32 IUNVEL 33 KUNIT -1 -
NSAVC 1000 NSAVV 00 NPRINT 1000 ISEED 314159 -
SGLD TSGAVG 0.2 TEMPSG 1.0 -
TBATH 300 FIRST 260 -
IASORS 0 IASVEL 1 ICHECW 0 -
NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSWIT -
CUTNB 14.0 CTOFNB 13.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.0
4) SGMD simulation with a constant guiding temperature of 1 K.
! Perform SGMD simulation
DYNA LEAP STRT CPT NSTE 1000000 TIME 0.002 -
IPRFRQ 10000 ISVFRQ 1000 IHTFRQ 0 IEQFRQ 0 INBFRQ 10 IHBFRQ 0 -
IUNREA -1 IUNWRI 31 IUNCRD 32 IUNVEL 33 KUNIT -1 -
NSAVC 1000 NSAVV 00 NPRINT 1000 ISEED 314159 -
SGMD TSGAVG 0.2 TEMPSG 1.0 -
TCON TCOU 0.1 TREF 300 -
FIRST 260 -
IASORS 0 IASVEL 1 ICHECW 0 -
NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSWIT -
CUTNB 14.0 CTOFNB 13.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.0
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute