[gmx-users] mdrun error

[Justin Lemkul]

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

-- 
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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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