Nancy wrote:
<snip>
I then proceed to enlarge the box and solvate the molecule:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p
ethanediol.top -shell 1
So, instead of filling the box, you are simply specifying a shell of water
around your ethanediol? Have you tried just filling the box to see if this
works? I'm wondering if equilibration is failing due to vacuum space in the
cubic box you specify with edticonf. Is your ethanediol centered in the box?
You haven't used -c with editconf.
I then use grompp to configure the minimisation:
$ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr
This is my .mdp file for minimisation:
===============================
define = -DPOSRE
Turn off position restraints. They don't serve much purpose in EM except to
potential interfere with the relaxation of bad geometry.
<snip>
If I proceed to equilibration after doing the above, the water molecules
simply fly apart (although not immediately). Additionally, it seems
that there are no interactions between the waters during equilibration.
Never plow ahead with such large forces. It is generally a waste of time. The
flying apart could be due to voids in the box, as I guessed above.
I have tried to run the minimisation for a larger number of steps, but
it does not help. I have also tried to delete individual water
molecules from the structure files, but doing so simply causes the
minimisation to "fixate" on another two molecules. I am not sure what
values of the energies are reasonable for this system, and how to
minimise it further. Please advise.
The potential energy will be proportional to the number of atoms in the system.
Without knowing that, we don't know what will be reasonable, either :) What
is for sure is that Fmax is far too large. Perhaps some of the above comments
will lead you in the right direction.
-Justin
Thank you.
Nancy
On Thu, Aug 6, 2009 at 8:38 AM, Bruce D. Ray <bruced...@yahoo.com
<mailto:bruced...@yahoo.com>> wrote:
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy
<nancy5vi...@gmail.com <mailto:nancy5vi...@gmail.com>> wrote:
> 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:
>
> ==========================
> define = -DFLEXIBLE
> integrator = steep
> emtol = 1000.0
> emstep = 0.01
> nsteps = 5000
>
> nstlist = 1
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> rvdw = 1.3
> pbc = xyz
>
> pme_order = 4
> constraints = none
>
> nstxout = 1
> nstvout = 1
> nstenergy = 1
> nstlog = 1
> ==========================
>
> $ mdrun -v -deffnm em
>
> 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
> ==========================
{remainder snipped}
The energies do seem large. What happens if you do energy minimization
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
*From:* Nancy <nancy5vi...@gmail.com <mailto:nancy5vi...@gmail.com>>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
*Sent:* Wednesday, August 5, 2009 10:28:47 PM
*Subject:* [gmx-users] Energy Minimisation and Equilibration
Problems
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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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