OLD Langevin Dynamics

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Description of Langevin Dynamics

Langevin dynamics (LD) is similar to molecular dynamics (MD) simulations except the LD simulations apply frictional drag based on the collision frequency (set by the FBETa scalar) to the atoms. In self-guided Langevin dynamics (SGLD), there is also a guiding force, which is a momentum-derived force that pushes atoms. Because of this factor, more conformations will be sampled in a given interval and thus it should only be used if determining the timescale in which events occur is not important.

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