Basic Langevin Dynamics Script
Please read the Basic MD Script section before continuing on the Langevin Dynamics. The "DYNA" command is used to run both Langevin dynamics and molecular dynamics, so the script will look similar to that one.
Before starting the "DYNA" command, the friction coefficient (expressed as collisions per picosecond) must be read in by CHARMM. This tutorial will use a value of 60 (the approximate collision frequency of water at room temperature). "SCALar FBETa SET 60.0 SELEct ALL END" will apply the friction force to the entire system.
Using the same MD script as in the molecular dynamics tutorial, change the "DYNA" command by adding "LANG" after "DYNA". The "SGLD" subcommand should be used for SGLD.
Langevin dynamics should not be used with constant pressure and temperature (CPT) so change "CPT" to "LEAP". Since the "PCONS" and "HOOVer" subcommands are related to CPT, remove them. Langevin dynamics has its own temperature control so the Nose-Hoover thermostat is not required.
The input script should look like the following:
* Langevin Dynamics
*
bomlev -2
! Read in Topology and Parameter files
OPEN UNIT 1 CARD READ NAME top_all27_prot_na.rtf
READ RTF CARD UNIT 1
CLOSE UNIT 1
OPEN UNIT 1 CARD READ NAME par_all27_prot_na.prm
READ PARA CARD UNIT 1
CLOSE UNIT 1
OPEN READ UNIT 2 CARD NAME 1yjp-full-min.psf
READ PSF CARD UNIT 2
CLOSE UNIT 2
OPEN READ UNIT 2 CARD NAME 1yjp-full-min.crd
READ COOR CARD UNIT 2
CLOSE UNIT 2
SHAKe BONH PARAm
SCAL FBETA SET 60.0 SELE ALL END
OPEN WRITE UNIT 41 CARD NAME new_1yjp-11213-ld.res
OPEN WRITE UNIT 31 FILE NAME new_1yjp-11213-ld.dcd
! print initial energy
ENERgy
DYNA LANG LEAP STRT -
TIMEstep 0.001 - !timestep in picoseconds
NSTEp 1000 - !number of steps and energy evaluations
NPRInt 100 - !step frequency for writing in kunit and printing
!energy on unit 6
IUNWri 41 - !unit to write restart file
IUNCrd 31 - !unit to write coordinated (unformatted)
IUNRea -1 - !unit to read in restart file
KUNIt -1 - !unit to write temperature and total energy
NSAVc 10 - !frequency for writing coordinates
NSAVv 10 - !frequency for writing velocities
IHBFrq 0 - !frequency to regenerate hydrogen bond list
INBFrq 25 - !lists updated when necessary (heuristic test)
ISEEd 314159 - !seed for the random number generator in assigning
!velocities
NBXMod 5 - !Add 1-2 1-3 and special 1-4 interactions
ATOM - !electrostatics calculation (default) is done on
!atom-atom basis
CDIE - !energy ~ 1/r
FSWItch - !use switching
VATOm - !needed for nonbond list generation
VSWItch - !use switching function for van der Waals
CUTNb 16.0 - !distance cutoff for neighbor list
CTOFnb 12.0 - !max distance for pair to consider in energy
CTONnb 8. - !Distance at which smoothing function reduces
!pair's contribution
INBFrq -1 - !lists updated when necessary (heuristic test)
EPS 1. - !dielectric potential
E14FAC 1.0 - !electrostatic scale factor
WMIN 1.0 - !warning cutoff for minimum atom-atom distance
TBATh 300 - !temperature of heath bath
FIRStt 300 - !initial temperature of the system
FINAlt 300 - !final temperature of the system
TEMInc 10.0 - !value to increase temperature by
IASOrs 1 - !assign (NOT scale) velocities during heating/equil
IASVel 1 - !use gaussian distribution of velocities
ISCVel 1 - !single scale factor
ICHEcw 0 - !checks if avg temp. lies within a window
TWINdh 0.0 !Highest deviation allowed of FINALT on the
!high side
OPEN UNIT 1 CARD WRITE NAME new_1yjp-11213-ld.pdb
WRITE COOR PDB UNIT 1
* PDB Coords
*
OPEN UNIT 1 CARD WRITE NAME new_1yjp-11213-ld.crd
WRITE COOR CARD UNIT 1
* Coords
*
OPEN UNIT 1 CARD WRITE NAME new_1yjp-11213-ld.psf
WRITE PSF CARD UNIT 1
* PSF
*
STOP
|