# AWH assertion failed error

**URL:** <https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722>\
**Category:** User discussions\
**Tags:** awh\
**Created:** [June 30, 2023, 3:39pm UTC](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722 "2023-06-30T15:39:38Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![FelipeRM](https://avatars.discourse-cdn.com/v4/letter/f/d26b3c/32.png) [@FelipeRM](https://gromacs.bioexcel.eu/u/FelipeRM)\
**Post date:** [June 30, 2023, 3:39pm UTC](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722/1 "2023-06-30T15:39:38Z")

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GROMACS version: 2023.1  
GROMACS modification: No

Hello! I am trying to run an AWH simulation of a DNA/RNA hybrid molecule. My pull groups are two atoms in the backbone of the RNA in adjacent nucleotides, the reaction co-ord is the distance between these atoms. My goal is to create a pmf curve along this co-ordinate. The issue is that after I run this simulation for some time, I get the error:

Program: gmx mdrun, version 2023.1  
Source file: src/gromacs/applied\_forces/awh/pointstate.h (line 355)  
Function: gmx::PointState::updateFreeEnergy(const gmx::BiasParams&, double)::\<lambda()\>  
MPI rank: 0 (out of 2)

Assertion failed:  
Condition: std::abs(freeEnergy\_) \< detail::c\_largePositiveExponent  
Very large free energy differences or badly normalized free energy in AWH  
update.

There are several things I’ve tried to fix this issue:

1. Lowered dt to 0.001 from 0.002
2. Ran my minimization and equilibration steps with a double precision build of gromacs
3. Lowered my emtol parameter during minimization to 100 from 1000
4. added vdw-modifier = Potential-shift to my simulation mdp

Otherwise I am using the mdp files produced by charmm-gui and the awh tutorial on the gromacs site. I am using amber force fields but that hasn’t been an issue before.  
No matter the parameters I run it with, the awh simulation will always run for about 70 ns before encountering this error. When i run the same system without awh I can reach 200 ns no problem. I know 70 ns is plenty, im just concerned ive set something up wrong in the awh simulation which is causing the error.

Any insights are appreciated, thanks!

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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:** [July 24, 2023, 2:09pm UTC](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722/2 "2023-07-24T14:09:31Z")

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Could you post your AWH mdp parameters?

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<div class="post-metadata">

**Author:** ![FelipeRM](https://avatars.discourse-cdn.com/v4/letter/f/d26b3c/32.png) [@FelipeRM](https://gromacs.bioexcel.eu/u/FelipeRM)\
**Post date:** [July 24, 2023, 6:05pm UTC](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722/3 "2023-07-24T18:05:03Z")

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Here is the mdp as I would like it to work and how I originally tried the simulation, thank you for any comments!

integrator = md  
dt = 0.002 ;  
nsteps = 100000000  
nstxtcout = 50000  
nstvout = 50000  
nstfout = 50000  
nstcalcenergy = 100  
nstenergy = 1000  
nstlog = 1000  
;  
cutoff-scheme = Verlet  
nstlist = 20  
vdwtype = Cut-off  
vdw-modifier = None ;  
DispCorr = EnerPres  
rvdw = 0.9  
rlist = 0.9  
rcoulomb = 0.9  
coulombtype = PME  
;  
tcoupl = Nose-Hoover  
tc\_grps = SOLU SOLV  
tau\_t = 1.0 1.0  
ref\_t = 303.15 303.15  
;  
pcoupl = Parrinello-Rahman  
pcoupltype = isotropic  
tau\_p = 5.0  
compressibility = 4.5e-5  
ref\_p = 1.0  
;  
constraints = h-bonds  
constraint\_algorithm = LINCS  
continuation = yes  
;  
nstcomm = 100  
comm\_mode = linear  
comm\_grps = SOLU SOLV  
;  
pull = yes ; The reaction coordinate (RC) is defined using pull coordinates.  
pull-ngroups = 2 ; The number of atom groups needed to define the pull coordinate.  
pull-ncoords = 1 ; Number of pull coordinates.  
pull-nstxout = 5000 ; Step interval to output the coordinate values to the pullx.xvg.  
pull-nstfout = 0 ; Step interval to output the applied force (skip here).

pull-group1-name = Oxygen43 ; Name of pull group 1 corresponding to an entry in an index file.  
pull-group2-name = Phosphate44 ; Same, but for group 2.

pull-coord1-groups = 1 2 ; Which groups define coordinate 1? Here, groups 1 and 2.  
pull-coord1-geometry = distance ; How is the coordinate defined? Here by the COM distance.  
pull-coord1-type = external-potential ; Apply the bias using an external module.  
pull-coord1-potential-provider = awh ; The external module is called AWH!  
;  
awh = yes ; AWH on.  
awh-nstout = 50000 ; Step interval for writing awh\*.xvg files.  
awh-nbias = 1 ; One bias, could have multiple.  
awh1-ndim = 1 ; Dimensionality of the RC, each dimension per pull coordinate.  
awh1-dim1-coord-index = 1 ; Map RC dimension to pull coordinate index (here 1–\>1)  
awh1-dim1-start = 0.10 ; Sampling interval min value (nm)  
awh1-dim1-end = 0.60 ; Sampling interval max value (nm)  
awh1-dim1-force-constant = 128000 ; Force constant of the harmonic potential (kJ/(mol\*nm^2))  
awh1-dim1-diffusion = 5e-5 ; Estimate of the diffusion (nm^2/ps)  
;

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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:** [July 25, 2023, 10:30am UTC](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722/4 "2023-07-25T10:30:23Z")

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My guess is that a minimum distance of 0.1 nm leads to extremely high energies and forces which could cause instabilities in the simulation.