[gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie

[Hassan Shallal]

Dear Gromacs users,
 
I ran a production MD simulation on a ligand in a water box. I used NVT with coloumb and vdw cut-offs and avoided using PME. I analyzed the .edr file using g_lie after the simulation was finished, I found that at all the time steps, the energy was 0 KJ/mol, is that normal? How come the energy of the system is 0? 
'
I am including both the simulation mdp file and the output of g_lie for inspection...
 
I would appreciate if I could get any feedback about the reasons for this problem. 
Regards
 
Hassan Shallal
University of the Pacific
Stockton, CA 95211
 
The mdb file:
 
------------------------------------------------------------------------------------------------------------------------------------------------------------------
;RUN CONTROL PARAMETERS =
integrator          =  md       ; production
tinit               =  0        ; starting time for your run (only makes sense for integrators md, sd and bd)
dt                  =  0.002    ; ps !
nsteps              =  2500000  ; total 5 ns.
nstcomm             =  1        ; frequency for center of mass motion removal
;OUTPUT FREQUENCY OPRIONS FOR COORDINATES, VELOCITIES, AND FORCES = (because this is equilibration, we don't want to waste hard disk storgae space)
nstxout                  = 1000    ; frequency to write coordinates to output trajectory file, the last coordinates are always written
nstvout                  = 1000    ; frequency to write velocities to output trajectory, the last velocities are always written
nstfout                  = 0    ; frequency to write forces to output trajectory.
;OUTPUT FREQUENCY OPRIONS FOR ENERGIES =
nstlog                   = 2500 ; frequency to write energies to log file, the last energies are always written
nstenergy                = 1000 ; frequency to write energies to energy file, the last energies are always written
;NEIGHBOR SEARCHING PARAMETERS =
nstlist             =  10       ; neighbor list update frequency
ns_type             =  grid     ; ns algorithm (simple or grid)
pbc                 =  xyz      ; periodic boundary conditions (xyz or none)
rlist               =  1        ; cut-off distance of the short-range neighbor list (nm)
domain-decomposition = no
;OUTPUT FREQUENCY AND PRESISION FOR XTC FILES =
nstxtcout                = 5000  ; frequency to write coordinates to xtc trajectory (STEPS)
xtc-precision            = 1000  ; precision to write to xtc trajectory
energygrps               = SOL UNK 
;OPTIONS FOR ELECTROSTATIC AND VDW =
coulombtype         =  Cut-off  ; method of doing electrostatics (Twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb,
where rcoulomb ? rlist.)
rcoulomb_switch     =  0        ; where to start switching the Coulomb potential (nm)
rcoulomb            =  1        ; distance for Coulomb cut-off (nm)
epsilon_r           =  1        ; the relative dielectric constant (1 or zero, if zero, means infinity)
vdwtype             =  Cut-off  ; method of doing VDW (Twin range cut-off's with neighbor list cut-off rlist and VdW cut-off rvdw, where
rvdw ? rlist.)
rvdw                =  1        ; distance for LJ or Buckingham cut-off (nm)
DispCorr            =  no       ; Don't apply long range dispersion corrections for Energy and Pressure
;OPTIONS FOR TEMPERATURE COUPLING = 
Tcoupl              =  v-rescale 
tau_t               =  0.1            ; time constant for coupling in ps (one for each group in tc grps), 0 means no temperature coupling
tc_grps             =  System         ; to avoid hot solvent cold solute situation
ref_t               =  298.15       
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = no
pcoupltype               = isotropic   ; Isotropic pressure coupling with time constant
tau_p                    = 0.5         ; time constant for coupling in ps
compressibility          = 4.5e-05     ; compressibility for water at 1 atm and 300 K
ref_p                    = 1.0         
-------------------------------------------------------------------------------------------------------------------------------------------------------------------
The .xvg g_lie output file:
------------------------------------------------------------------------------------------------------------------------------------------------------------------
# This file was created Fri May 21 17:21:18 2010
# by the following command:
# g_lie -f 4_pr_NVT.edr -o 4_pr_NVT.xvg 
#
# g_lie is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@    title "LIE free energy estimate"
@    xaxis  label "Time (ps)"
@    yaxis  label "DGbind (kJ/mol)"
@TYPE xy
         0           0
         2           0
         4           0
         6           0
         8           0
        10           0
        12           0
        14           0
        16           0
        18           0
        20           0
        22           0
all the way until
  5000           0
         0           0
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