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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