On 10/31/12 4:10 AM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
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..
Note that EM is not run in time, so your settings below are misleading. The
only settings that matter are nsteps and emstep; dt is ignored completely when
running EM. Note that your cutoff settings are incorrect for Gromos96, as you
say you are using. How did you generate the HFIP topology?
The positive potential indicates that your system has a net repulsive energy, so
the configuration isn't very happy. The maximum force is very good, but there
may be unsatisfied interactions that yield the positive energy. Perhaps a
gentle equilibration will resolve the situation.
-Justin
My mdp file was like this :
;
; Preprocessing
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
;
; Electrostatics
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
experiment.
Thanks in advance u guys,
--
Best Regards,
Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : [email protected]
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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