README FOR SAGUARO

 To Install Saguaro : Type ./install.sh
 The Install shell will place executable files in Saguaro?.?/exe
 Where ?.? denotes the version. Make sure this is in your path.

 To Make Saguaro : Type make all

 Quick Go - The Basic Command To Run Saguaro is :
            Saguaro.x -i Options.in -c Sys.gf2k -p Sys.parm -m Sys.mol
                      -x Answer -v Velc -e Energy -r Restart -o Output

 SEE Saguaro?.?/tutorial for explinations on how to run various simulations

 FILE DISCRIPTIONS

 Options.in is a namelist format (Like AMBER) to input the simulation options
 See OPTIONS For a Discription of Options and Default Values

 Sys.gf2k is the coordinates of the system

 Sys.parm is the parameter file for the system

 Sys.mol is the molecule data file for the system

 Traj is the outputed Coordinates of the atoms at user specified times

 Velc is the Outputed Velocities of the atoms at user specified times

 Energy - File that contains Outputed Energies from the simulation
          NOTE - THI FORMAT OF THIS FILE IS SIMULATION DEPENDANT

 Restart - File that contains information needed to restart the simulation.
           NOTE - THE FORMAT OF THIS FILE IS SIMULATION DEPENDANT

 Output - File that contains Saguaro's Output messages

 You Can Make Sys.crd Sys.parm and Sys.mol by using amber2saguaro.x This 
 Program Converts an amber parameter and coordinate file to the saguaro format

 FILE FORMATS

 COORDINATE FILE

 Format(I8,E16.8) NAT,TIME
 Number of Atoms, System Time(ps)

 Format(I3,3F13.7)TYPE(i),X(i),Y(i),Z(i)  i=1,NAT
 Atomic Number , Atom Coordinates(Ang)

 Format(3F13.7)ax(i),ay(i),az(i) i=1,3   
 Direct Lattice Vectors(Ang)

 If there are velocities then the format is

 Format(I8,E16.8) NAT,TIME
 Format(I3,6F13.7)TYPE(i),X(i),Y(i),Z(i),Vx(i),Vy(i),Vz(i)
 Foramt(3F13.7)ax(i),ay(i),az(i)

 PARAMETER FILE

 Format(7I8)NAT,NBD,NHBD,NAG,NDH,NEX,N14
 Number of Atoms, Bonds, Bonds w HYD, Angles, Dihedrals, Excluded, 1-4

 Format(4E16.8)MASS(i),Q(i),R(i),EPS(i) i=1,NAT
 Atom Masses in AMU, Charges in #e, VDW Radius (Ang), VDW well Depth(ev)

 Format(2I8,16x,2E16.8)ATM1(i),ATM2(i),KB(i),REQ(i) i=1,NBD
 1st Atom in Bond, 2nd, Spring Const.(ev/Ang^2), Eq. Bond Length (Ang)
 BONDS CONTAINING HYDROGEN MUST BE LISTED FIRST

 Format(3I8,8x,2E16.8)ATM1(i),ATM2(i),ATM3(i),KTH(i),TEQ(i) i=1,NAG
 1st Atom in Angle, 2nd, 3rd, Spring Const.(ev), Eq. Angle (Degrees)

 Format(4I8,3E16.8)ATM1(i),ATM2(i),ATM3(i),ATM4(i),V(i),GAM(i),N(i) i=1,NDH
 1st Atom, 2nd, 3rd, 4th, Potential (ev), Eq. Angle (Degrees), Multiplicity

 Format(2I8)ATM1(i),ATM2(i) i=1,NEX
 List of excluded Atom interactions Each Pair occurs only once.
 MUST ALSO INCLUDE 1-4 PAIRS

 Format(2I8)ATM1(i),ATM2(i) i=1,N14
 List of 1-4 Interactions Each Pair occurs only once

 MOLECULE FILE

 Format(I8,I6)NAT,NMOL
 Number of Atoms, Number of Molecules

 Format(I6,2X,A1) MOLN(i),TYPE(i) i=1,NAT
 Molecule Number, Type (S= SOLVANT C= COUNTER ION A= ART/"ACTIVE"/SOLUTE)

 Format(I6) NADH
 Number of ART Dihedrals

 Format(4I6) LADH(i,1),LADH(i,2),LADH(i,3),LADH(i,4) i=1,NADH
 List of Atom Numbers in each ART Dihedral

 ENERGY FILE (Simulation Dependant)

 Format(9A12)TITLES
 Format(9F12.4)TIME,EB,EA,ED,EC,EV,EK,ET,TEMP
 System Time(ps), Bond Energy, Angle Energy, Dihedral Energy
 Coulomb Energy, VDW Energy, Kinetic Energy, Total (ev), Temperature(k)

 VELOCITY FILE

 Format(I8,E16.8)NAT,TIME
 Format(I3,F13.7)ITYPE(i),Vx(i),Vy(i),Vz(i), i=1,NAT
 Atom Type, Atomic Velocities (Ang/ps)

 TRAJECTORY FILE (Simulation Dependant)

 Format(I8,E16.8)NAT,TIME
 Format(I3,F13.7)ITYPE(i),X(i),Y(i),Z(i), i=1,NAT
 Atom Type, Atomic Coordinates (Ang)

 Format(3F13.7)ax(i),ay(i),az(i) i=1,3
 Direct Lattice Vectors (Ang)

 RESTART FILE (Simulation Dependant)

 
END README
