INSTRUCTIONS FOR THE MOLECULAR DYNAMICS TUTORIAL
PEPTIDE IN A WATERBOX

This tutorial will demonstrate how to set up a
system to run a molecular dynamics simulation
with periodic boundary conditions of a small
peptide in a box of water.

There are 3 main steps that need to be followed.

1) Create Saguaro parameter, coordinate, and molecule files
2) Minimize the structure
3) Equilibrate the waterbox to appropriate temperature and pressure

After step 3, the resulting coordinates are prepared for a MD run.

STEP 1
This can be performed in three ways:
1) create parameter files "by hand" (NOT RECOMENDED)
2) use xleap GUI in AMBER to make amber top and crd files
   then convert to saguaro using Amber2saguaro.x tool
3) use pepalyze or... if you simply want generic parameters
   (no charges just a few standard springs and VDW parameters)
   use GenericP.x

Parameter, coordinate, and molecule files have already been created
for you .... they are pepwb.parm pepwb.gf2k and pepwb.mol

STEP 2
1) First get (or make) an options.in file that specifies what
   options you will be running for the simulation
   This file has been created for you .... optmin.in
2) Run Sagauro.x The command to use here is:

   Saguaro.x -i optmin.in -p pepwb.parm -c pepwb.gf2k -m pepwb.mol \
             -r pepwb_min.gf2k -e pepwb_min.ene -o pepwb_min.out

   The -r tells Sagauro to put the final structure coordinates in the
   file pepwb_min.gf2k for restarting later and the -e is to specify
   the energy file, the -o is for the output file.
   The output file contains all information about the simulation
   and any errors that may have occured during the execution.

STEP 3
1) First get (or make) an options.in file for the equilibration procedure.
   This file has been created for you .... opteq.in
   You can either equilibrate in the canonical ensemble (NVT) or
   any other ensemble that you like (NPT) (NVE) (NPH) etc.
   We will equilibrate in the constant pressure constant temperature
   ensemble here (NPT) to get better lattice vectors.
2) Run Saguaro.x The command here is:

   Saguaro.x -i opteq.in -p pepwb.parm -c pepwb_min.gf2k -m pepwb.mol \
             -r pepwb_eq.gf2k -e pepwb_eq.ene -o pepwb_eq.out

Now you should have the final files

pepwb.parm pepwb.mol pepwb_eq.gf2k

These are your starting files for an MD run.

To run MD simply use the optmd.in options file (this options file
is similar to opteq.in except it specifies to output the peptides
trajectory every so often with option NSC = 100)
The MD run can now run the canonical ensemble (NVT) since the
pressure has been equilibrated.

type on the command line:

   Saguaro.x -i optmd.in -p pepwb.parm -c pepwb_eq.gf2k -m pepwb.mol \
             -r pepwb_md.gf2k -x pepwb_traj.gf2k -e pepwb_md.ene \
             -o pepwb_md.out

The additional -x tells saguaro to place the trajectory in the file
pepwb_traj.gf2k

ECD 3/12/07

END TUTORIAL
