The thermodynamic integration program is using similar connectivity and 
coordinate files (coordinates are in CHARMM format) to run normal Verlet MD.
Output files are standard output that contains info on the simulation
progress, velocity and coordinate files (CHARMM dynamics format).


Below is a sample input

~TEST FOR VALINE DIPEPTIDE
~
~debug
file conr name=(wcon.fir.mut)       unit=10 read
file conp name=(wcon.fin.mut)       unit=11 read
file rcrd name=(1.CRD)              unit=14 read
file wcrd name=(MUT50-60.DCD) bina unit=12 wovr
file wvel name=(MUT50-60.VCD) bina unit=13 wovr
#ste=1000 #equ=900 #pri=50 #wcr=1000 list=20 #tes=50 newv=1100
#eqv=1 #sve=1 rand=-3451187 step=0.001   
temp=300. 
rmax=9.0 epsi=1. cdie  shif v14f=8. e14f=2. shkb
firs=50.d-2 fina=60.d-2 sted=10.d-2 
action

The "bina" keyword in the file lines means that the file should be
opened unformatted. Parameters that come after the file lines
include normal energy parameters (e.g. rmax epsi) and the file energy.prog
should be consulted for those. In addition simulation parameters
include:

PARAMETERS FOR THERMODYNAMIC PERTURBATION 

file conr name=(wcon.fir.mut)  -
wcon.fir.mut - connectivity file which contains all parameters of the
initial state
file conp name=(wcon.fin.mut)  -
wcon.fin.mut - connectivity file which contains all parameters of the
final state
In input example connectivity files are the same except (just for test purposes,
without any additional physical sense) charges of N and O and lengh of
bond CA-CB. 
charg
temp              temperature
#ste              number of integration steps
#pri              print each #pri steps
#win              number of of the LAMBDA segments +1 during perturbation
		  from LAMBDA=0 to LAMBDA=1
firs              initial value of  LAMBDA 
fina              final value of  LAMBDA 
sted              step  of  LAMBDA 
in input example firs=0.5 fin=0.6 and sted=0.1
This means that during calculation two windows are under consideration
[0.5,0.6] and [0.6,0.7]
If user wants to run only one window let's say from 0.1 to 0.2
the firs and fin parameters should be the same and equal 0.1.
With sted=0.1 program will run window [0.1,0.2]
#wcr              coordinates are written at step interval #wcr
#eqv        velocity scaling at step interval #eqv during equilibration period
#sve        velocity scaling at step interval #sve after  equilibration period
step        step size
#tes       period for checking constraints 
#equ       number of thermalization steps 
newv       select new velocities each newv  steps
rand       initial seed for random vel. selection


The line with "action" is self explanatory

Below is an input sample
~TEST FOR VALINE DIPEPTIDE
~
~debug
file conr name=(wcon.fir.mut)       unit=10 read
file conp name=(wcon.fin.mut)       unit=11 read
file rcrd name=(1.CRD)              unit=14 read
file wcrd name=(MUT50-60.DCD) bina unit=12 wovr
file wvel name=(MUT50-60.VCD) bina unit=13 wovr
#ste=1000 #equ=900 #pri=50 #wcr=1000 list=20 #tes=50 newv=1100
#eqv=1 #sve=1 rand=-3451187 step=0.001   
temp=300. 
rmax=9.0 epsi=1. cdie  shif v14f=8. e14f=2. shkb
firs=50.d-2 fina=60.d-2 sted=10.d-2 
action

Below is a sample dyna output obtained from the benchmark run

current cons difference- current free energy difference due to
SHAKE constraints
current free difference - current free energy difference after current
number of steps
free energy difference - the final of value of free energy difference at
selected window
current variance - variance calculated at current step


therm> ~TEST FOR VALINE DIPEPTIDE
therm> ~
therm> ~debug
therm> file conr name=(wcon.fir.mut)       unit=10 read
therm> file conp name=(wcon.fin.mut)       unit=11 read
therm> file rcrd name=(1.CRD)              unit=14 read
therm> file wcrd name=(MUT50-60.DCD) bina unit=12 wovr
therm> file wvel name=(MUT50-60.VCD) bina unit=13 wovr
therm> #ste=1000 #equ=900 #pri=50 #wcr=1000 list=20 #tes=50 newv=1100
therm> #eqv=1 #sve=1 rand=-3451187 step=0.001
therm> temp=300.
therm> rmax=9.0 epsi=1. cdie  shif v14f=8. e14f=2. shkb
therm> firs=50.d-2 fina=60.d-2 sted=10.d-2
therm> action

  PARAMETERS FOR THERMODYNAMIC PERTURBATION :

  temperature: 300.0
  number of integration steps:    1000
  print each      50 steps
  initial value of  LAMBDA :     .50000
  final value of  LAMBDA :     .60000
  step  of  LAMBDA :     .10000
  data is on unit:     6 coordinates are on unit    12
  initial coordinates are read from unit :    14
  Coordinate are read in CHAR style 
  coordinates are written at step interval :  1000
  velocity scaling at step interval of:     1
  step size:   .100E-02
  period for checking constraints    50
  number of thermalization steps    900
  select new velocities each   1100 steps
  initial seed for random vel. selection   -3451187
  debug ?  F

  All bonds will be shaked 

  Number of shake constraints =  13
 Number of degf (exc. shake)      29
getcrd> * title for CHARMM coordinates
getcrd> *
 current temperature is      420.150
  Number of particle pairs  40
 first energy at the remote point  -3.43734272614591
  *********************************** 
  energy sampled at the position  .6
  *********************************** 
 first energy at the original point -9.75788455197974
  ************************************* 
  energy sampled at the position  .5
  ************************************* 
  first energy difference  6.32054182583383
 ***************************************** 
 ***  END OF TRAJECTORY INITIALIZATION *** 
 ***************************************** 
  Number of particle pairs  40
  *** equlibration period *** 
  *** scaling velocities at step  1
  current temperature is  238.2154328694411
  desired temperature is  300.0
  scaling factor =  1.12221399483026
  *** equlibration period *** 
  *** equlibration period *** 
  *** scaling velocities at step  3
  current temperature is  326.5465165801963
  desired temperature is  300.0
  *** equlibration period *** 
 **** checking energy conservation **** 
  at step  50 total energy is  14.58236049533251
  tot. pot.  5.48462420718091 total kine.  9.09773628815161
  **** PRINTING  INFO  **** 
 energy at the remote point 2.48538296303882
 energy at the original point 5.48462420718091
  Kinetic Energy   .9098E+01
  Potential Energy (1)  .5485E+01
  Potential Energy Difference (2)-(1)    -2.999
  Total Energy   .1458E+02
 current temperature is   315.660
  **** PRINTING  INFO **** 

   ++++++++++++++ SOME INFO REMOVED ++++++++++++++

  **** PRINTING  INFO **** 
  free energy difference  -2.02273682291102
  partition function variance  7.199790374545545E-03