[gmx-users] mdrun error

rose rahmani rose.rhmn93 at gmail.com
Mon May 21 23:43:32 CEST 2018

I have sheet(at z=0) and 2wall(are close to each other and one of them
begins at z=3.5 and the other at z=~3.8) structures which the other
molecules(water, AA, NA, CL) are BETWEEN sheet and wall structures. before
solvation, i add box size without considering the wall in coordination
because i didn't want that sol molecules enter the space between two carbon
WALLs. After solvation in EM step because of PBC issues i had to increase
the box size in x dimension for 0.094 nm. The box size in z dimension is
almost 3times bigger than the distance between walls and sheet ( box
size=12 nm) because of PBC.

I try to figure out what happens and please correct me if i am wrong;
1, as i can see in .gro file 3 water molecules are in vaccum space so may
feel larger force.

2, some water molecules are between to carbon walls(maybe they could get
there because of 0.094nm space that i added to x dimension)

3, number of water molecules is not enough for this size of system.

4, i know that the system in energy minimization (before pulling) minimized
with minus Kj/mol and didn't fluctuate, but GROMACS said in didn't get

5, i constraint hbonds and because of that i decided to choose dt=2fs. As
far as i know hbonds have the highest vibrational frequency and least
time.... so i choose 2fs...

Could you please help me which one caused to problem?


On Tue, 22 May 2018, 01:19 Justin Lemkul, <jalemkul at vt.edu> wrote:

> On 5/21/18 4:47 PM, rose rahmani wrote:
> > Hi,
> >
> > I do umbrella sampling with GROMACS4.5.4 version. I got this error
> > "A charge group moved too far between two domain decomposition steps."
> > But when i try it in another computer(version 4.5.4 was also installed
> > there) this error doesn't exist any more! How could it be possible?which
> > one is correct?
> Welcome to the stochastic nature of MD. You have an unstable system that
> occasionally works. Don't trust it - figure out where the instability
> comes from and/or prepare the system more gently.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
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