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

[Justin A. Lemkul]

Hassan Shallal wrote:
> 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...
>  

What was your g_lie command?  The default values of -Elj and -Eqq are zero. 
Based on your energygrps (SOL and UNK), you are inherently defining the 
interactions between the solvent and UNK as zero unless you are setting some 
other value.

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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