OLD Langevin Dynamics
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