[gmx-users] Energy cal from MD simulations

[Lod King]

Hi,

I have obtained a 100 ns simulation using Amber. I would like to calculate
the potential energy (VDW, COUL,ect) from the trajectory, below is my
command.

$gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o
rerun.tpr -maxwarn 1

$gmx mdrun -rerun ../protein.trr -s rerun.tpr -g rerun.log -e rerun.edr

$gmx energy -f rerun.edr -o test.xvg

My question is: in this test.mdp file, should I specify any parameters that
should be the same as I used when running MD using Amber.


 Run parameters

integrator      = md

nsteps          = 500000        ;

dt              = 0.002         ; 2 fs

; Output control

nstxout         = 10000         ;

nstvout         = 10000         ;

nstfout         = 0             ;

nstxtcout       = 1000          ;

;nstxout-compressed = 1000      ;

nstenergy       = 1000          ;

nstlog          = 10000         ;

; Constraints

constraint_algorithm = lincs    ;

constraints     = hbonds        ; d

lincs_iter      = 1             ;

lincs_order     = 4             ;

continuation    = yes           ;

; Neighborsearching

cutoff-scheme   = Verlet        ;

verlet-buffer-tolerance = 0.005 ;

ns_type         = grid          ;

nstlist         = 20            ;

rlist           = 1.0           ;

rcoulomb        = 1.0           ;

rvdw            = 1.0           ;

; Electrostatics

coulombtype     = PME           ;

pme_order       = 4             ;

fourierspacing  = 0.16          ;

; Temperature coupling is on

tcoupl          = V-rescale     ;

tc-grps         = System        ;

tau_t           = 0.1           ;

ref_t           = 300           ;

pcoupl          = Parrinello-Rahman     ;

pcoupltype      = isotropic     ;

tau_p           = 2.0           ;

ref_p           = 1.0           ;

compressibility = 4.5e-5        ;

pbc             = xyz           ;

DispCorr        = EnerPres      ;

gen_vel         = no

pull            = no