[gmx-users] Problem to compute interaction energy between different groups

[Justin Lemkul]

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

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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