# Fatal Error in Steered MD simulation

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-in-steered-md-simulation/4528>\
**Category:** User discussions\
**Tags:** mdp-parameters, simulation-setup\
**Created:** [July 28, 2022, 6:16pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-in-steered-md-simulation/4528 "2022-07-28T18:16:13Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Hasan](https://avatars.discourse-cdn.com/v4/letter/h/df705f/32.png) [@Hasan](https://gromacs.bioexcel.eu/u/Hasan)\
**Post date:** [July 28, 2022, 6:16pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-in-steered-md-simulation/4528/1 "2022-07-28T18:16:13Z")

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GROMACS version: 2021.3  
GROMACS modification: No

Hi everyone,  
I am currently running steered MD simulation and it always gives the following error:

Fatal Error Distance between pull groups 1 and 2 (4.402440 nm) is larger than 0.49 times  
the box size (4.402299).

The center of mass of MEMB is 4.60 nm and the center of mass of NPH is 6.88 nm. I tried changing the pull code with different options but it gave the same error. I am providing the mdp file below (the one I am currently using), thinking that you guys can help me. I would appreciate any suggestion. Thank you,

integrator = md  
dt = 0.002  
nsteps = 10000000  
nstxout = 50000  
nstvout = 50000  
nstfout = 50000  
nstcalcenergy = 100  
nstenergy = 1000  
nstlog = 1000  
nstxout-compressed = 500  
;  
cutoff-scheme = Verlet  
nstlist = 20  
rlist = 1.2  
vdwtype = Cut-off  
vdw-modifier = Force-switch  
rvdw\_switch = 1.0  
rvdw = 1.2  
coulombtype = PME  
rcoulomb = 1.2  
;  
tcoupl = Nose-Hoover  
tc\_grps = MEMB SOLV NPH  
tau\_t = 1.0 1.0 1.0  
ref\_t = 310.15 310.15 310.15  
;  
pcoupl = Parrinello-Rahman  
pcoupltype = semiisotropic  
tau\_p = 5.0  
compressibility = 4.5e-5 4.5e-5  
ref\_p = 1.0 1.0  
;  
constraints = h-bonds  
constraint\_algorithm = LINCS  
continuation = yes  
;  
freezegrps = NPH  
freezedim = Y Y N  
;  
nstcomm = 100  
comm\_mode = linear  
comm\_grps = System  
;  
pull = yes  
pull\_ncoords = 1 ; only one reaction coordinate  
pull\_ngroups = 2 ; two groups defining one reaction coordinate  
pull\_group1\_name = MEMB  
pull\_group2\_name = NPH  
pull\_coord1\_type = umbrella ; harmonic potential  
pull\_coord1\_geometry = cylinder ; simple distance increase  
pull\_coord1\_vec = 0.0 0.0 1.0  
pull\_coord1\_dim = N N Y ; pull along z  
pull-cylinder-r = 1.5 ;  
pull-coord1-init = 2.0 ;  
pull\_coord1\_groups = 1 2 ; groups 1 and 2 define the reaction coordinate  
pull\_coord1\_start = no ; define initial COM distance \> 0  
pull\_coord1\_rate = -0.005 ; 0.01 nm per ps = 1 nm per ns  
pull\_coord1\_k = 1000 ; kJ mol^-1 nm^-2

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [July 29, 2022, 12:16pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-in-steered-md-simulation/4528/2 "2022-07-29T12:16:19Z")

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Hi,  
I guess you are pulling between large group. In this case the mdp option `pull-pbc-ref-prev-step-com` may help (see more here [Non-equilibrium pulling — GROMACS 2022.2 documentation](https://manual.gromacs.org/current/reference-manual/special/pulling.html)).  
\Alessandra

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<div class="post-metadata">

**Author:** ![Hasan](https://avatars.discourse-cdn.com/v4/letter/h/df705f/32.png) [@Hasan](https://gromacs.bioexcel.eu/u/Hasan)\
**Post date:** [July 29, 2022, 4:03pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-in-steered-md-simulation/4528/3 "2022-07-29T16:03:58Z")

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Hi Alessandra,  
Thank you for your reply. I am using `pull_coord1_geometry` cylinder, which the manual says that the `pull-group1-pbcatom` option is not used to activate `pull-pbc-ref-prev-step-com`. What would you suggest?

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [August 5, 2022, 12:19pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-in-steered-md-simulation/4528/4 "2022-08-05T12:19:38Z")

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I would think that the distance that mdrun reports is correct, so you are pulling to far.

At what simulation time do you get this error?