[gmx-users] Problem to compute interaction energy between different groups
Justin Lemkul
jalemkul at vt.edu
Fri Nov 24 17:02:18 CET 2017
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
==================================================
More information about the gromacs.org_gmx-users
mailing list