Protocol Sheet: ACETK.EQ

Equilibration of a globular protein in the Charmm forcefield

Author: Gianni De Fabritiis (acemd@googlegroups.com)
Copyrights 2010-2011, University Pompeu Fabra. All rights reserved.
Version: v1

Software requirements: ACEMD.1782, VMD.1.8.7 (These are the versions on which it was tested)
Knowledge requirements: Use of VMD, ACEMD manual
Input requirements: This protocol assumes that you have already built a solvated system in the Charmm forcefield starting from a PDB file. Here, we provide the files structure.pdb and structure.psf for a solvated SH2 complex which you should substitute with yours. If you have not build your system yet, please refer to protocol ACETK.BLDCHARMM. Also, par_all27_prot_na.inp is used as an example, you might want to choose another version of the Charmm forcefield.

Download ACETK.EQ.v1

acetk.eq.v1
|-- build
|   |-- get_celldimension.vmd
|   |-- set_constraints.vmd
|   |-- structure.pdb
|   `-- structure.psf
|-- equil
|   |-- input.npt
|   |-- input.nve
|   `-- par_all27_prot_na.inp
`-- run
    `-- input

Disclaimer. This protocol is based on a best practice. In no way, we guarantee that it is optimal for your system. You use it at your own risk.

STEP1: Prepare the system

Modify the PDB with the atom selection on which to apply initial equilibration constraints and measure the periodic box of the system.

1) Copy into the build directory structure.pdb and structure.psf with the solvated model.

2) Edit select_constraints.vmd to decide the atoms on which to apply an initial positional harmonic restraint. Usually the heavy atoms of the protein and maybe crystal waters, it will protect the experimental conformation from the strong forces which act during the first phases of the equilibration. Equilibration position are taken from the coordinates of the atoms and strength of harmonic restraints from the beta column.

  #overwrite structure.pdb to set 1 on the beta column for each atom to be restrained. 
  vmd -dispdev text -e set_constraints.vmd

3) Execute get_celldimension to get the dimensions of the periodic cell box. The last line of the output "celldimension XX YY ZZ" will be required in the input.nve of next step.

  vmd -dispdev text -e get_celldimension.vmd

STEP2: Minimization, thermalization and pressure equilibration

Relax the initial structure preserving the experimental structure to the correct temperature and pressure.

1) Copy pdb, psf files into equil directory

  #Current working directory "equil"
  cp ../build/structure.psf ../build/structure.pdb .

2) Insert the correct celldimension into input.nve.
3) Minimize and thermalize the system with a constrain on heavy atoms using the ACEMD configuration file input.nve. Make sure you add your values for the celldimension variable in the input file.

  acemd input.nve

4) Equilibrate the pressure without constraints

  acemd input.npt

STEP3: Production run

Run production simulations.

1) Copy pdb, psf, parameter, coordinate, velocity and box dimension files into run directory

  #Current working directory "run"
  cp ../equil/structure.psf ../equil/structure.pdb ../equil/par_all27_prot_na.inp .
  cp ../equil/npt.coor ../equil/npt.vel ../equil/npt.xsc .

2) Edit input to decide length of simulation and set celldimension to the new values from npt.xsc
3) Run

  acemd input