On 11/24/17 11:00 AM, ARNAB MUKHERJEE wrote:
Hello,
I have simulated a system of DNA and Protamine (Coarse grained, Martini). I
want to look at the interaction energy between different groups like DNA -
Protamine, DNA - ions, etc. I have defined energy groups in the mdp file,
and I pass the index file with the groups while building the tpr file.
After the run is complete, when I run gmx energy command, no matter what
interaction energy I choose, it always gives me 0 (for all time steps). But
the total Potential energy works. I am not able to understand why?
If your run used a GPU, then this is what you will get; pairwise energy
decomposition is not supported on GPU.
Use mdrun -rerun to recompute the energies using CPU only. There is
anyway no point in wasting time having mdrun calculate interaction
energies during the run.
-Justin
This is how my .mdp file looks like :
title = NVT equilibration with position restraint on all solute
(topology modified)
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 60000000 ; 1 * 500000 = 500 ps
;nsteps = 5000
dt = 0.01 ; 1 fs
; Output control
nstxout = 0 ; save coordinates every 10 ps
nstvout = 0 ; save velocities every 10 ps
nstcalcenergy = 50
nstenergy = 1000 ; save energies every 1 ps
nstxtcout = 2500
;nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps
; nstxout-compressed replaces nstxtcout
;compressed-x-grps = System ; replaces xtc-grps
nstlog = 1000 ; update log file every 1 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds)
constrained
;lincs_iter = 2 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
epsilon_r = 15
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 20 fs
rvdw_switch = 1.0
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
vdwtype = Cut-off ; Twin range cut-offs rvdw >= rlist
;vdw-modifier = Force-switch
;Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = v-rescale
tc_grps = System
tau_t = 1.0
ref_t = 300
energygrps = DNA Protein W ION
freezegrps = DNA
freezedim = Y Y Y
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correctiion
DispCorr = no ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell
distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 50
comm-mode = Linear
comm-grps = System
;
refcoord_scaling = com
I would greatly appreciate any help.
Thanks in advance,
Thanks and Regards,
Arnab Mukherjee
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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