(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2013

AMBER Advanced Tutorial 17
SECTION 1

Umbrella Sampling Example
Calculating the PMF for Alanine Dipeptide Phi/Psi Rotation

By Ross Walker & Thomas Steinbrecher

1) Generating and Relaxing the Initial Structure

The first thing we need to do is generate an initial structure and relax this so that we can use it as the input for the umbrella sampling runs themselves. Typically one would obtain such a structure from a pdb file. However, in our case the system is simple enough that we can use leap's sequence command to build it:

$AMBERHOME/bin/tleap
> source leaprc.ff99SB
> mol = sequence { ACE ALA ALA NME }
> solvateoct mol TIP3PBOX 10.0
> saveamberparm mol ala_tri.prmtop ala_tri.inpcrd

Files: ala_tri.prmtop, ala_tri.inpcrd

Since this is a small system we don't have to be overly gentle in our heating and relaxation. What we will do is:

  1. Minimize (1000 steps)
  2. Heat (NVT, 0 to 300K, 20ps)
  3. Relax (NPT, 300K, 100ps)
01_min.in 02_heat.in 03_equil.in
minimize
 &cntrl
  imin=1, maxcyc=1000, ncyc=500,
  cut=8.0, ntb=1, ntp=0,
  ntc=2, ntf=2,
 /
heat NVT 20ps
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=10000, dt=0.002,
  ntc=2, ntf=2, cut=8.0,
  ntt=3, gamma_ln=1.0,
  ntb=1, ntp=0,
  tempi=0.0, temp0=300.0,
  ntpr=100, ntwx=100, ntwr=10000,
  ioutfm=1,
 /
equil NPT 100ps
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=50000, dt=0.002,
  ntc=2, ntf=2, cut=8.0,
  ntt=3, gamma_ln=1.0,
  ntb=2, ntp=1, tautp=1.0,
  temp0=300.0,
  ntpr=500, ntwx=500, ntwr=10000,
  ioutfm=1,
 /

We can now run these through pmemd. For example to run them using 2 processors on a dual cpu desktop:

mpirun -np 2 $AMBERHOME/bin/pmemd.MPI -O -i 01_min.in -o 01_min.out -p ala_tri.prmtop -c ala_tri.inpcrd -r 01_min.rst

mpirun -np 2 $AMBERHOME/bin/pmemd.MPI -O -i 02_heat.in -o 02_heat.out -p ala_tri.prmtop -c 01_min.rst -r 02_heat.rst -x 02_heat.nc

mpirun -np 2 $AMBERHOME/bin/pmemd.MPI -O -i 03_equil.in -o 03_equil.out -p ala_tri.prmtop -c 02_heat.rst -r 03_equil.rst -x 03_equil.nc

File: 01_min.out, 01_min.rst, 02_heat.out, 02_heat.rst, 02_heat.nc, 03_equil.out, 03_equil.rst, 03_equil.nc

You should check the results here to make sure the system remained stable etc. You should also notice that the alanine tripeptide remains in the trans configuration. We can now go to the next section and set up the umbrella sampling simulations.


CLICK HERE TO GO TO SECTION 2


(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2013