# Error in md run nvt step

**URL:** <https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435>\
**Category:** User discussions\
**Created:** [January 13, 2021, 1:40pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435 "2021-01-13T13:40:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\
**Post date:** [January 13, 2021, 1:40pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435/1 "2021-01-13T13:40:24Z")

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When I run the command: gmx mdrun -deffnm 06\_nvt

Error: step 2: 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  
Segmentation fault (core dumped)

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**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:** [January 13, 2021, 3:03pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435/2 "2021-01-13T15:03:54Z")

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[https://manual.gromacs.org/current/user-guide/terminology.html#blowing-up](https://manual.gromacs.org/current/user-guide/terminology.html#blowing-up)

If you want more detailed help, you’ll have to provide far more detail: what is your system, how did you prepare it, what was the outcome of energy minimization, upload your `.mdp` files, etc.

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<div class="post-metadata">

**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\
**Post date:** [January 13, 2021, 5:22pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435/3 "2021-01-13T17:22:06Z")

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Thanks for reply  
I did docking of selected compounds I opened the docked pose in mgt tools and saved it by clicking on write current and converted it in pdb file, then submitted to PRODRG Server to get the topology files… I then opened the receptor file in note pad and deleted the RNA primer (as i took rna bound protein as target for docking) and saved the file as protein And I have attached the mdp files for your reference. Note: it saved the files in step.pdb in the folder after using md run nvt steps

ions.mdp  
; LINES STARTING WITH ‘;’ ARE COMMENTS  
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 10.0 kJ/mol  
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  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)  
coulombtype = PME ; Treatment of long range electrostatic interactions  
rcoulomb = 1.0 ; long range electrostatic cut-off  
rvdw = 1.0 ; long range Van der Waals cut-off  
pbc = xyz ; Periodic Boundary Conditions

em.mdp

; LINES STARTING WITH ‘;’ ARE COMMENTS  
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 10.0 kJ/mol  
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  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)  
coulombtype = PME ; Treatment of long range electrostatic interactions  
rcoulomb = 1.0 ; long range electrostatic cut-off  
rvdw = 1.0 ; long range Van der Waals cut-off  
pbc = xyz ; Periodic Boundary Conditions

nvt.mdp

title = Protein-ligand complex NVT equilibration  
define = -DPOSRES ; position restrain the protein and ligand  
; Run parameters  
integrator = md ; leap-frog integrator  
nsteps = 100000 ; 2 \* 100000 = 200 ps  
dt = 0.002 ; 2 fs  
; Output control  
nstxout = 500 ; save coordinates every 1.0 ps  
nstvout = 500 ; save velocities every 1.0 ps  
nstenergy = 500 ; save energies every 1.0 ps  
nstlog = 500 ; update log file every 1.0 ps

; Bond parameters  
continuation = no ; first dynamics run  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = all-bonds ; all bonds (even heavy atom-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 cells  
nstlist = 10 ; 20 fs, largely irrelevant with Verlet  
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  
tcoupl = V-rescale ; modified Berendsen thermostat  
tc-grps = Protein\_DRG Water\_and\_ions ; two coupling groups - more accurate  
tau\_t = 0.1 0.1 ; time constant, in ps  
ref\_t = 300 300 ; reference temperature, one for each group, in K  
; Pressure coupling  
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 = 300 ; temperature for Maxwell distribution  
gen\_seed = -1 ; generate a random seed

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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:** [January 13, 2021, 6:07pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435/4 "2021-01-13T18:07:08Z")

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Don’t use PRODRG. Its topologies are demonstrably unsuitable for MD simulations and it was never intended for this purpose.

Try again with a more reliable ligand topology (ATB for GROMOS, or choose a different force field entirely and generate the topology accordingly), and if you’re still having issues, follow the page I linked above which specifically describes how to diagnose an unstable protein-ligand complex.

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<div class="post-metadata">

**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\
**Post date:** [January 14, 2021, 2:06pm UTC](https://gromacs.bioexcel.eu/t/error-in-md-run-nvt-step/1435/5 "2021-01-14T14:06:41Z")

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Thank you sir to suggest the ATB but it gave error about geometry, i used avogadro to add hydrogen and geometry optimization. I tried a lot but could not get the ligand topology. I don’t know what should I do now. Could you please help to sort it out ?