[gmx-users] mdrun error

Justin Lemkul jalemkul at vt.edu
Mon May 21 23:47:14 CEST 2018

On 5/21/18 5:42 PM, rose rahmani wrote:
> !!!
> 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
> converged.
> 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?

It could be any number of things, perhaps even things not listed here. 
Be a scientist - change one thing at a time until you uncover the source 
of the problem. As it stands, your system has far too many variables to 
assign blame to any one of them.



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


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