# The cut-off length is longer than half the shortest box vector or longer than the smallest box diago

**URL:** <https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161>\
**Category:** User discussions\
**Created:** [November 28, 2020, 5:47am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161 "2020-11-28T05:47:00Z")\
**Posts on this page:** 17\
**Page:** 1

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**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [November 28, 2020, 5:47am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/1 "2020-11-28T05:47:00Z")

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How should the box size be increased ?  
Since I am very new to Gromacs, kindly help…  
I find we have to use editconf command with -d option…  
Should I change the box vectors ?  
For eg:  
If this is the actual command,  
gmx editconf -f complex.gro -o complex\_newbox.gro -c -box 6.41840 6.44350 6.59650  
changing it to  
gmx editconf -f complex.gro -o complex\_newbox.gro -c -d 1.5 -box 6.41840 6.44350 6.59650  
is correct ?

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [November 28, 2020, 11:21pm UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/2 "2020-11-28T23:21:01Z")

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So you have this error when youuse gmx grompp???  
What is your rvdw in mdp file??? In most force field it is 1.0 or 1.2 etc  
It’s very strange that you have this error when you have 6x6x6 box.  
For example if you have in you mdp file rvdw=1. Your box should be min 2x2x2 (each dimension two times bigger than rvdw)

If you want have a bigger box just define a bigger box.  
Instead of  
gmx editconf -f complex.gro -o complex\_newbox.gro -c -box 6.41840 6.44350 6.59650

Try this  
gmx editconf -f complex.gro -o complex\_newbox.gro -c -box 8.41840 8.44350 8.59650  
and you will have bigger box (2 nm longer in x,y,z dimension).

To be honest I never used -d option. You can read that  
-d (0)  
Distance between the solute and the box  
With `-d` and a `triclinic` box the size of the system in the _x_ -, _y_ -, and _z_ -directions is used. With `-d` and `cubic` , `dodecahedron` or `octahedron` boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance

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**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [November 29, 2020, 4:23pm UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/3 "2020-11-29T16:23:28Z")

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Sir,  
I did as you said…  
For me rvdw = 1.2, so I added 2.4 to the existing box vectors and applied in editconf command but the same error appeared during shrinking iterations…  
I tried with -d 1.5, again the same error after 4 th iteration …so am really confused as I couldnt find the root of the error

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<div class="post-metadata">

**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [November 30, 2020, 12:45am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/4 "2020-11-30T00:45:56Z")

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Please copy and paste the actual output from the `gmx editconf` command. There is some other information that is printed out by the command that should assist with working out what is going on here.

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [November 30, 2020, 2:50am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/5 "2020-11-30T02:50:39Z")

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Hello sir,

This is the command and output …Its a prot-lig system and the lig topology is gen using PRODRG server.

gmx editconf -f complex.gro -o complex1\_newbox.gro -c -box 8.81840 8.84350 8.99650

Read 7589 atoms  
Volume: 681.651 nm^3, corresponds to roughly 306700 electrons  
No velocities found  
system size : 6.618 8.981 11.469 (nm)  
center : 5.097 5.597 6.025 (nm)  
box vectors : 6.618 8.981 11.468 (nm)  
box angles : 90.00 90.00 90.00 (degrees)  
box volume : 681.65 (nm^3)  
shift : -0.688 -1.175 -1.526 (nm)  
new center : 4.409 4.422 4.498 (nm)  
new box vectors : 8.818 8.844 8.997 (nm)  
new box angles : 90.00 90.00 90.00 (degrees)  
new box volume : 701.60 (nm^3)

.mdp file is given below

minim.mdp - used as input into grompp to generate em.tpr  
; Parameters describing what to do, when to stop and what to save  
define = -DSTRONG\_POSRES -DSTRONG\_POSRES\_LIG ; Prevent protein AND ligand from moving  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 1000.0 kJ/mol/nm  
emstep = 0.01 ; Energy step size  
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions  
nstlist = 1 ; Frequency to update the neighbor list and long range forces  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)  
coulombtype = cutoff ; Treatment of long range electrostatic interactions  
rcoulomb = 1.2 ; Short-range electrostatic cut-off  
rvdw = 1.2 ; Short-range Van der Waals cut-off  
pbc = xyz ; Periodic Boundary Conditions

Also, while generating the system.gro, I pasted the new box vectors at the bottom…that is 8_8_8 dimension and removed the 6_6_6 vectors…

Thank you in advance…

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 30, 2020, 5:32pm UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/6 "2020-11-30T17:32:38Z")

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A few things here.

> [@gromacsash](#):
>
> gmx editconf -f complex.gro -o complex1\_newbox.gro -c -box 8.81840 8.84350 8.99650

> [@gromacsash](#):
>
> system size : 6.618 8.981 11.469 (nm)

Your assigned box vectors are inconsistent with the actual size of the system. Clearly your system is much larger along the z-axis than you’re trying to assign it, and that will just create problems.

You should not need to do any manual assignment or changing of box vectors when using InflateGRO, which I’m assuming is what you’re doing. Start over. Post the original error message you get and don’t manipulate the box. We should be able to help you sort out the original error without going down another unproductive rabbit hole.

> [@gromacsash](#):
>
> Its a prot-lig system and the lig topology is gen using PRODRG server.

PRODRG is an unreliable source for ligand parameters. Your simulation will be deeply flawed at best, and entirely wrong at worst. If you want GROMOS parameters, use ATB.

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 1, 2020, 4:50am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/7 "2020-12-01T04:50:29Z")

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Hello Justin  
Thank you so much for the timely response…  
I will try as suggested and post the message.

**Regarding usage of ATB server**

I tried using ATB server (already read various responses on how to use ATB files) where I have couple of queries like,  
The format to be used …GROMOS or GROMACS ?  
Bcz in GROMACS format, we have united atom ITP and united atom PDB(original geo) files and in  
GROMOS96 format, we have united atom MTB and united atom PDB (original geo) files.  
I read that MTB file should not be used on account of some charge calculation disparity…  
Which should be chosen ?  
Also, I get “atom type not found” while using the ATB gen files ?

Pardon me if am wrong in any of the above statements and hope to seek a clarity on these …

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 1, 2020, 5:25am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/8 "2020-12-01T05:25:09Z")

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Hello,

The following is the error that I get when I run the iterations (third run) without changing any of the box vectors…Here I didnt use the bash script for automation…  
In a previous run of the same file with automation, I got the output but when I take it for NVT, I got the error “segmentation fault, core dumped”, with too many LINCS warning…I was trying to sort out that error when I ended up on reasons like 1) energy not minimised properly or 2) fault in ligand topology or 3) error in nvt.mdp file…

Command line:  
gmx grompp -f minim\_inflategro.mdp -c system\_inflated3.gro -p topol.top -r system\_inflated3.gro -o system\_inflated3\_em.tpr

NOTE 1 [file minim\_inflategro.mdp]:  
With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note  
that with the Verlet scheme, nstlist has no effect on the accuracy of  
your simulation.

Setting the LD random seed to -1227739524  
Generated 813 of the 2346 non-bonded parameter combinations  
Excluding 3 bonded neighbours molecule type ‘Protein’  
Excluding 3 bonded neighbours molecule type ‘PDB’  
Excluding 3 bonded neighbours molecule type ‘DPPC’

NOTE 2 [file topol.top, line 47383]:  
System has non-zero total charge: -19.000000  
Total charge should normally be an integer. See  
[http://www.gromacs.org/Documentation/Floating\_Point\_Arithmetic](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic)  
for discussion on how close it should be to an integer.

ERROR 1 [file topol.top, line 47383]:  
ERROR: The cut-off length is longer than half the shortest box vector or  
longer than the smallest box diagonal element. Increase the box size or  
decrease rlist.

Removing all charge groups because cutoff-scheme=Verlet

There were 2 notes

* * *

Program: gmx grompp, version 2018.8  
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)

Fatal error:  
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS  
website at [http://www.gromacs.org/Documentation/Errors](http://www.gromacs.org/Documentation/Errors)

Thank you for being patient …

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 1, 2020, 5:50am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/9 "2020-12-01T05:50:48Z")

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Also, I didn’t face any error for my apoprotein simulation, I mean I used bash script automation there…

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [December 1, 2020, 6:14pm UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/10 "2020-12-01T18:14:20Z")

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You need GROMACS-formatted files to use in GROMACS. If you have missing atom types, consult the ATB FAQ, I bet they address this issue…

Regarding the error from `grompp`, please share your `minim_inflategro.mdp` and `system_inflated3.gro` files. You may need to post to Google Drive, Dropbox, etc. and provide us the link.

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 2, 2020, 7:42am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/11 "2020-12-02T07:42:12Z")

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> **[Meet Google Drive – One place for all your files](https://accounts.google.com/ServiceLogin?service=wise&passive=1209600&continue=https:%2F%2Fdrive.google.com%2Ffile%2Fd%2F1i-DHCqkR-WpS-H0Cb4gQTEOjGyyNdrBt%2Fview?usp%3Dsharing&followup=https:%2F%2Fdrive.google.com%2Ffile%2Fd%2F1i-DHCqkR-WpS-H0Cb4gQTEOjGyyNdrBt%2Fview?usp%3Dsharing)**

> **[Meet Google Drive – One place for all your files](https://accounts.google.com/ServiceLogin?service=wise&passive=1209600&continue=https:%2F%2Fdrive.google.com%2Ffile%2Fd%2F19Do3jAa_wdR6cnHVhi2ofsAfjqKi-nwt%2Fview?usp%3Dsharing&followup=https:%2F%2Fdrive.google.com%2Ffile%2Fd%2F19Do3jAa_wdR6cnHVhi2ofsAfjqKi-nwt%2Fview?usp%3Dsharing)**

Here are the links …

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [December 2, 2020, 11:11am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/12 "2020-12-02T11:11:34Z")

</div>

The links are restricted. Please make them accessible.

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 2, 2020, 11:48am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/13 "2020-12-02T11:48:13Z")

</div>

I hope the files can now be accessed.  
Thank you…

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [December 2, 2020, 4:24pm UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/14 "2020-12-02T16:24:04Z")

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Look at `system_inflated3.gro` in a text editor. It is completely misformatted. Not just the box vectors but the coordinates themselves. I have no idea how that would have happened but you should back up and start over without any manual manipulations or changes. If you have further issues, please post a complete accounting of all your commands, exactly as entered, especially the InflateGRO commands including the scaling factors and relevant screen output from running InflateGRO.

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 7, 2020, 10:42am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/15 "2020-12-07T10:42:22Z")

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I startef from first and did E minimisation and once I put the system for nvt equilibration, I got the following errors…  
Can anyone pls. tell where exactly this error points to ?

Forcefield used : Gromos96  
Membrane prot-lig system in dppc  
I used bash script automation for shrinking till the total area is 70 Ang sq.units and I got energy minimisation as

Steepest Descents converged to Fmax \< 1000 in 5118 steps  
Potential Energy = -1.9396520e+05  
Maximum force = 9.2956146e+02 on atom 3723  
Norm of force = 3.6939106e+01

Command line:  
gmx mdrun -v -deffnm nvt

Compiled SIMD: None, but for this host/run AVX2\_256 might be better (see log).  
The current CPU can measure timings more accurately than the code in  
gmx mdrun was configured to use. This might affect your simulation  
speed as accurate timings are needed for load-balancing.  
Please consider rebuilding gmx mdrun with the GMX\_USE\_RDTSCP=ON CMake option.  
Reading file nvt.tpr, VERSION 2018.8 (single precision)  
Changing nstlist from 12 to 100, rlist from 1.2 to 1.252

Using 1 MPI thread  
Using 8 OpenMP threads

WARNING: Using the slow plain C kernels. This should  
not happen during routine usage on supported platforms.  
Setting the maximum number of constraint warnings to 2147483647  
starting mdrun ‘protcut - hbond-opt in water’  
50000 steps, 100.0 ps.  
step 100, will finish Fri Dec 4 12:59:44 2020  
WARNING: Listed nonbonded interaction between particles 2174 and 2179  
at distance 2.994 which is larger than the table limit 2.252 nm.

This is likely either a 1,4 interaction, or a listed interaction inside  
a smaller molecule you are decoupling during a free energy calculation.  
Since interactions at distances beyond the table cannot be computed,  
they are skipped until they are inside the table limit again. You will  
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is  
probably something wrong with your system. Only change the table-extension  
distance in the mdp file if you are really sure that is the reason.

My nvt.mdp file is as below (Pls correct me wherever wrong)

title = NVT equilibration for DPPC\_Protein\_LIG  
define = -DPOSRES -DPOSRES\_LIG ; position restrain the protein  
; Run parameters  
integrator = md ; leap-frog integrator  
nsteps = 50000 ; 2 \* 50000 = 100 ps  
dt = 0.002 ; 2 fs  
; Output control  
nstxout = 100 ; save coordinates every 0.2 ps  
nstvout = 100 ; save velocities every 0.2 ps  
nstenergy = 100 ; save energies every 0.2 ps  
nstlog = 100 ; update log file every 0.2 ps  
; Bond parameters  
continuation = no ; first dynamics run  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = h-bonds ; H bonds constrained  
lincs\_iter = 1 ; accuracy of LINCS  
lincs\_order = 4 ; also related to accuracy  
; Neighborsearching  
cutoff-scheme = Verlet  
ns\_type = grid ; search neighboring grid cels  
nstlist = 10 ; 10 fs  
rlist = 1.2 ; short-range neighborlist cutoff (in nm)  
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)  
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)  
; Electrostatics  
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.16 ; grid spacing for FFT  
; Temperature coupling is on  
tcoupl = V-rescale ; modified Berendsen thermostat  
tc-grps = DPPC\_Protein\_LIG Water\_and\_ions ; two coupling groups - more accurate  
tau\_t = 0.1 0.1 ; time constant, in ps  
ref\_t = 323 323 ; reference temperature, one for each group, in K  
; Pressure coupling is off  
pcoupl = no ; no pressure coupling in NVT  
; Periodic boundary conditions  
pbc = xyz ; 3-D PBC  
; Dispersion correction  
DispCorr = EnerPres ; account for cut-off vdW scheme  
; Velocity generation  
gen\_vel = yes ; assign velocities from Maxwell distribution  
gen\_temp = 323 ; temperature for Maxwell distribution  
gen\_seed = -1 ; generate a random seed  
; COM motion removal  
; These options remove motion of the protein/bilayer relative to the solvent/ions  
nstcomm = 100  
comm-mode = Linear  
comm-grps = DPPC\_Protein\_LIG Water\_and\_ions

Hope to get some help,  
Thank you in advance

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<div class="post-metadata">

**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [December 7, 2020, 10:44am UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/16 "2020-12-07T10:44:32Z")

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After the above warnings, the following appeared…

step 200: One or more water molecules can not be settled.  
Check for bad contacts and/or reduce the timestep if appropriate.  
Wrote pdb files with previous and current coordinates  
step 200, will finish Fri Dec 4 12:59:36 2020Segmentation fault (core dumped)

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [December 7, 2020, 2:34pm UTC](https://gromacs.bioexcel.eu/t/the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diago/1161/17 "2020-12-07T14:34:56Z")

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What is the source of your ligand topology? How have you validated it?

Follow the steps here to diagnose:

> **[Terminology — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system)**