[gmx-users] Problem in energy minimization

[Jin J.C]

Dear Justin,
My protocol is simply like this:
1. Prepare the system of protein embedded in a equilibrated pure DOPC
bilayer.
2. Make a rectangular box
gmx editconf  -f  protein-mem.gro  -o protein-mem-box.gro -box 14.6 14.6
16.3 -center 7.3 7.3 8.15
3. solvate
gmx solvate -cp protein-mem-box.gro -cs water-300k-1bar.gro -radius 0.21 -o
protein-mem-solvated.gro
4. grompp -f minimization.mdp -c protein-mem-solvated.gro -p
protein-mem-solvated.top -o minim-solvated.tpr
5. mdrun -deffnm minim-solvated

At begining, with this box size, 18880 water molecules were added.
And I met error when I ran step 5.

After modified the box size,
gmx editconf  -f  protein-mem.gro  -o protein-mem-box.gro -box 14 14 16
-center 7 7 8
there was added 18210 water molecules.

This is my mdp file for running minimization

title                    = Martini
integrator         = steep
dt                      = 0.02
nsteps              = 10

init_step            = 0
energygrps      = System
nstlog                = 10

cutoff-scheme   = group
nstlist                  = 10
ns_type              = grid
pbc                      = xyz
rlist                       = 1.4
coulombtype          = shift
rcoulomb_switch   = 0.0
rcoulomb                = 1.2
vdw-type                = shift
rvdw-switch           = 0.9
rvdw                       = 1.2

define                   = -DPOSRES

Cheer,
Jin

2015-06-05 15:33 GMT+09:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi Jin,
>
> Can you give the protocol you used in commands? And what are the box
> dimensions and how many solvent molecules were added?
>
> Cheers,
>
> Tsjerk
> On Jun 5, 2015 08:30, "Jin J.C" <jcjin.hcmut.001 at gmail.com> wrote:
>
> > Dear Justin,
> > I have tried to change the box size, make it smaller a little, solvate
> > again and then, the error is resolved. Actually, I don't understand the
> > reason. especially, I have no idea about the "impossible geometry" as you
> > mentioned. Can you give me a little explanation?
> > Thank you so much.
> > Jin.
> >
> > 2015-06-04 20:38 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 6/3/15 10:23 PM, Jin J.C wrote:
> > >
> > >> Dear all,
> > >> I am trying to set a coarse-grained MD for the membrane protein.
> > >> After solvating, I met an error when running a short energy
> > minimization (
> > >> 10 steps) before adding ions.
> > >>
> > >> Steepest Descents:
> > >> Tolerance (Fmax)   =  1.00000e+01
> > >> Number of steps    =           10
> > >> Step=   10, Dmax= 2.0e-05 nm, Epot=  2.76192e+20 Fmax=         inf,
> > atom=
> > >> 8872
> > >> Reached the maximum number of steps before reaching Fmax < 10 writing
> > >> lowest energy coordinates.
> > >> Steepest Descents did not converge to Fmax < 10 in 11 steps.
> > >> Potential Energy  =  2.7619190e+20
> > >> Maximum force    =           inf on atom 8872
> > >> Norm of force       =            inf
> > >>
> > >> The reason is because of Maximum force is equal to infinity.
> Therefore I
> > >> can not proceed further. Atom 8872 is water atom. Even when I delete
> > this
> > >> atom, the error occurs again with another water molecules, and goes
> on.
> > >>
> > >> Can someone help me figure out? and explain to me what happen?  Is
> this
> > >> because of overlapping problem?
> > >>
> > >>
> > > Likely.  You have some impossible geometry somewhere, or otherwise
> > > something is very wrong with the topology.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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