Hello dear community I simulate 2 surfaces of kaolinite with water and sodium chloride between these surfaces. When the simulation is done I want to calculate the z-profile of the sodium and chloride with gmx density but these message appear
Command line:
gmx density -f 5md -s 5md -o test
Reading file 5md.tpr, VERSION 2022.1 (single precision)
Select 1 group to calculate density for:
Group 0 ( System) has 26196 elements
Group 1 ( Other) has 6000 elements
Group 2 ( SUP) has 6000 elements
Group 3 ( NA) has 41 elements
Group 4 ( CL) has 1 elements
Group 5 ( Ion) has 42 elements
Group 6 ( SUP) has 6000 elements
Group 7 ( NA) has 41 elements
Group 8 ( CL) has 1 elements
Group 9 ( Water) has 20154 elements
Group 10 ( SOL) has 20154 elements
Group 11 ( non-Water) has 6042 elements
Group 12 ( Water_and_ions) has 20196 elements
Select a group: 3
Selected 3: âNAâ
Reading frame 0 time 0.000
Program: gmx density, version 2021.2
Source file: src/gromacs/pbcutil/mshift.cpp (line 809)
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 6042 atoms. The longest distance involved in such interactions
is 1.975 nm which is close to half the box length. This molecule type consists
of muliple parts, e.g. monomers, that are connected by interactions that are
not chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors â GROMACS webpage https://www.gromacs.org documentation
When I save my files I only save the non-Water atoms in the 5md files, hence the 6042, but It seems that It take like all my system is just one molecule. But the real system is one surfaces with 3000 atoms, a second surface with 3000 atoms, 41 Sodium ion, and 1 chloride ion.
The problem was that I included an artificial interaction like a planar dihedral because I simulate kaolinite on the 010 surface, to maintain the alignment of all the sheets, I included this dihedral which works, but it is a long range interaction and I create this problem when I tried to use gmx rdf.
So I only use this interaction in the equilibration steps and then remove it for the production step and problem solve.
Hey dear @gonzaloqe, I have almost encountered the same problem as you. Could you please explain in detail how you resolved this issue? Sorry for I am unable to fully understand your solution.
I am simulating the water and ions between the surfaces of two layers of alumina. After balancing under the NVT ensemble, I attempted to calculate some properties of water using gmx density and dipoles. At this point, I encountered the same error as you. I have tried many ways during this period, but I have not been able to solve it.
I canât understand what you mean by âartistic interactionâ and where it is reflected (such as whether it is a certain item in the .mdp file?). Could you explain more specifically?
Looking forward to your reply, thank you very much!
In my case i simulate kaolinite sheets, and in the equilibration steps they tend to deform. To overcome that problem I include an artificial planar dihedral like this in my itp files:
[ dihedrals ]
5 1996 225 1286 1 180 500.0 2
those atoms are not bonded they are from diferent sheets, hence the problem with a long distance interactions that gives me the error.
You need to find if there is a intramolecular interaction that is long as the half size of the box. then eliminate.
Maybe different resaons can lead to this âInconsistent shiftsâ error, since there is no dihedrals in my alumina itp file.
But your answer really helps me, since there is actually even no bond parameters in my itp file ( I use CLAYff, and it only defines bond parameters between O and H, alumina structure is only maintained by LJ parameters), so maybe this will cause the error.
My solution now is to make a .tpr and .xtc file without alumina (I only concern the water part), and in this case there is no âInconsistent shiftsâ error hahaha.
Again thanks a lot to your answer, it really helps me.