[gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie
Hassan Shallal
hshallal at PACIFIC.EDU
Mon May 24 10:39:14 CEST 2010
Dear Justin, Thanks alot for the feedback, I forgot to set the Clj and the Cqq and the ligand options for g_lie, I set them and I got the energy calculated and it is reasonable value. I am waiting to do the same thing for the whole complex (protein, ligand and sol) and get an estimate of the free energy of binding...
I still have a question for you and for other users who have done similar free energy calculations using g_lie, do the parameter file I include in this message seem fine? is there something that I missed and you or anyone else thinks I should have included?
Once again thanks alot for the feedback
The .mdp 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 =
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
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
________________________________
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Sun 5/23/2010 8:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie
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
> ------------------------------------------------------------------------------------------------------------
>
--
========================================
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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