[gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie
Justin A. Lemkul
jalemkul at vt.edu
Mon May 24 13:02:22 CEST 2010
Hassan Shallal wrote:
> 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?
>
The parameters you choose are based on the goals you should be setting at the
outset of the simulation. Using plain cutoffs is required for using g_lie, but
is otherwise discouraged due to artefacts. The parameters are syntactically
correct, no glaring errors, but whether or not they accomplish what you need is
something only you know.
-Justin
> 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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--
========================================
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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