CHARMM c33b2 sgld.doc
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Self-Guided Langevin Dynamics (SGLD) simulation
By Xiongwu Wu and Bernard R. Brooks
A SGLD simulation enhances conformational search efficiency through
acceleration of systematic motions in a molecular system. The systematic
motion represents the slow conformational change that contributes the most
in conformational search. A guiding force in the direction of the systematic
motion, which is calculated as a local average of velocities, is introduced
into the equation of motion to enhance the systematic motion. It has been
demonstrated that within the suggested parameter range, a SGLD simulation
has a dramatically enhanced conformational search efficiency while has little
perturbation on conformational distribution. More details are described in
the paper:
"Self-guided Langevin dynamcs simulation method", Chem. Phys. Letter,
381, 512-518(2003).
The SGLD algorithm is developed based on a previously developed
self-guided molecular dynamics simulation method, which employs a local
average of nonbonded interaction forces as the guiding force. The
force-based guiding force correlates with the energy surface that may
change the conformational distribution. The SGLD method uses a local
average of velocities to calculate the guiding force, and overcomes the
disadvantage of the old method. When SGLD is used without friction, we
refer to this method as SGMD. Please be not confused with the
force-based self-guided molecular dynamics method.
Two parameters, the guiding factor, SGFT, and the local average time,
TSGAVG, define the guiding effect in a SGLD simulation. A larger TSGAVG will
result in a slower motion to be enhanced. A larger SGFT will introduce
stronger guiding forces and result in a larger energy barrier overcoming
ability. When SGFT=0, a SGMD/SGLD simulaiton reduces to a normal MD/LD
simiulation. SGFT should be limited to keep systematic motion very small
as compared with thermo-motions like vibration, so that all degrees of
freedom retain their kinetic energies.
To avoid the difficulty in chosing the value of SGFT, a parameter
called guiding temperature (TEMPSG) is introduced. TEMPSG set the
perturbation limit that a guiding force may cause to a simulation system.
The guiding force will cause less perturbation than rising the temperature
by TEMPSG degrees. Normally, TEMPSG=1 K can provide significant enhancement
in conformational search, while cause a perturbation less than rising the
temperature by 1 degree. A larger TEMPSG results in more accelaration in
slow motion. When TEMPSG=0, a constant guiding factor, SGFT, will apply.
When TEMPSG>0, the guiding factors are calculated according to TEMPSG during
a SGMD/SGLD simulation. A user can monitor the instant SGFT and TEMPSG in
CHARMM output by setting PRNLEV>4.
* Menu:
* Syntax:: Syntax of the SGLD dynamics command
* Examples:: SGLD usage examples
File: Sgld -=- Node: Syntax
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[Syntax SGLD]
DYNAmics {LEAP {[LANG SGLD]} } ! SGLD simulation
{ {[CPT SGMD]} } ! SGMD simulation for a NPT ensemble
{ {[ SGMD]} sgld-spec]} ! SGMD simulation for a NVE ensemble
{ } other-dynamic-spec
sgld-spec::=[TSGAVG real] [TSGAVP real] {[TEMPSG real]} [SGMV] [ISGSTA] [ISGEND]
{[SGFT real] }
Keyword Default Purpose
SGLD false Turn on SGLD simulation (for Langevin dynamics, LANG).
Friction constants, FBETA, must be set at first.
SGMD false Turn on SGMD simulation (for MD simulations)
TSGAVG 0.2 ps Local average time. A larger TSGAVG will result in slower
motion to be enhanced. All motions with periods larger than
TSGAVG will be enhanced.
TSGAVP 10 ps Guiding effect average time. This time is used to calculate
averages to estimate SGFT from TEMPSG. A larger TSGAVP will
result in a slower flucturation of SGFT.
TEMPSG 1.0 K Guiding temperature. TEMPSG>0 will override SGFT. TEMPSG
set the perturbation limit a guiding force may cause to a
simulation system. The guiding force will cause less
perturbation than rising the temperature by TEMPSG degrees.
Normally, TEMPSG=1 K can provide significant enhancement in
conformational search, while cause a perturbation less than
rising the temperature by 1 degree. A larger TEMPSG results
in more accelaration in slow motion. When TEMPSG is set,
the guiding factors, SGFT, are calculated accordingly in a
SGMD/SGLD simulation.
SGFT 0.0 Guiding factor. When TEMPSG=0, SGFT will be
constant throughout a simulation. When TEMPSG>0,
SGFT fluctuates during the simulation to maintain a guiding
temperature of TEMPSG. If a constant SGFT simulation is
desired, one can read the approximate values of SGFT from
the output of a SGLD simulation with TEMPSG=1K.
SGMV false Allow guiding force on the center of mass
ISGSTA 1 The index of the first atom of the region to apply the
guiding force
ISGEND natom The index of the last atom of the region to apply the
guiding force
File: Sgld -=- Node: Examples
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Examples
1) SGLD simulation with default seting.
! 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 -
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 TEMPSG 1.0 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 factor.
! 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 0.0 SGFT 0.1 -
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 default setting.
! 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 -
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
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