[gmx-users] Why potential energy not in negative value?
Nur Syafiqah Abdul Ghani
pqah123 at gmail.com
Wed Oct 31 09:10:42 CET 2012
Currently I'm doing the minimization part for my solvent which is
hexafluoroisopropanol with water.
I'm packing them with packmol then use the forcefield gromos96.
Now by using the command
grompp -f em1.mdp -c minimize_301012.gro -p topol.top -o minimize_311012.tpr
mdrun -deffnm minimize_311012 -v
And its give the result as follow :
writing lowest energy coordinates.
Back Off! I just backed up minimize_311012.gro to ./#minimize_311012.gro.3#
Steepest Descents converged to Fmax < 15 in 36 steps
Potential Energy = 1.88042503678994e+05
Maximum force = 1.46843345643871e+01 on atom 30092
Norm of force = 1.94397813942079e+00
I already minimize it with the bigger step that use about 10ns.
Next I increase the step which take about 15ns and the result show
same as above..
My mdp file was like this :
title = STEEP
cpp = /usr/bin/cpp
include = -I/usr/local/gromacs/share/gromacs/top
define = -DFLEXIBLE
; Run Control
integrator = steep
nsteps = 75000000 ; 75000000 * 0.2 = 15000 ps = 15 ns
dt = 0.0002 ; 0.2 fs
; Energy Minimization
emstep = 0.0001 ; used with steep
emtol = 15
nstcgsteep = 500 ; do a steep every 10 steps of cg
energygrps = System
; Neighbor Searching
nstcomm = 1
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
rcoulomb-switch = 0
vdw-type = cut-off
rvdw = 1.2
rvdw-switch = 0
fourierspacing = 0.2
; Output Control
nstenergy = 10
optimize_fft = yes
; OPTIONS FOR BONDS
; OPTIONS FOR BONDS
constraints = none
Is the potential energy need to be in negative value for my simulation?
What happened if it not in negative value?Can I just proceed to the
next step for equilibration?
I already find and read the paper that relate to my simulation and
they did not mention the energy that they got from their
Thanks in advance u guys,
Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
alternative email : syafiqahabdulghani at gmail.com
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