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