Nancy wrote:
Hello,
I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started with an ethanediol mol2 file from which
topolbuild generated various files. I used editconf to enlarge to box
of the "ethanediol.gro" file:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
and then I used genbox to solvate it:
$ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
ethanediol_solv.gro -p ethanediol.top
I ran energy minimisation on it:
$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
my minim.mdp file is:
<snip>
and the energies converge (although I think that the values are still
too large for this system):
==========================
Steepest Descents converged to Fmax < 1000 in 12 steps
Potential Energy = -1.1206108e+04
Maximum force = 9.4016180e+02 on atom 31
Norm of force = 3.4989252e+02
==========================
This all seems reasonable to me.
<snip>
nsteps = 5000
dt = 0.0002
As I said before, 1 ps is too short to be meaningful for just about every
system.
rvdw = 1.3
Also, if using Gromos96, this value of rvdw is not strictly correct for this
force field.
the system "blows up". Addtionally, the structure of the solute is
incorrect (all atoms are bonded to each other).
Are you still getting LINCS warnings? If so, try "constraints = all-bonds"
instead of "constraints = all-angles." With respect to the "bonds" they are
simply an artefact of whatever visualization software you are using. Bonds are
not formed and broken in classical MD. Again I ask, when looking at the
trajectory, are you compensating for periodic boundary conditions properly using
trjconv?
-Justin
Please advise on how to minimise such a system further, and as to why
the equilibration is so unstable.
Thank you.
Nancy
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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