# Issue with GROMACS Simulation : MDP file parameters and NVT equilibration **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdp-parameters, simulation-setup\ **Created:** [March 30, 2025, 9:19am UTC](https://gromacs.bioexcel.eu/t/issue-with-gromacs-simulation-mdp-file-parameters-and-nvt-equilibration/11840 "2025-03-30T09:19:50Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![pritam\_biotech](https://avatars.discourse-cdn.com/v4/letter/p/919ad9/32.png) [@pritam\_biotech](https://gromacs.bioexcel.eu/u/pritam_biotech)\ **Post date:** [March 30, 2025, 9:19am UTC](https://gromacs.bioexcel.eu/t/issue-with-gromacs-simulation-mdp-file-parameters-and-nvt-equilibration/11840/1 "2025-03-30T09:19:50Z")
Dear GROMACS Community, I am encountering an issue with my GROMACS simulation, specifically when analyzing the output from the `gmx energy` command. I am running an NVT equilibration simulation using GROMACS version 2022, but the energy output suggests that the simulation might not have completed successfully or that there’s a problem with the energy file. Below, I’ve provided a detailed description of the problem, simulation settings, and troubleshooting steps I’ve taken so far. I’d greatly appreciate your insights! This is a simulation of Docked structure of two proteins\*\* ### Simulation Details - **GROMACS Version** : 2022 - **Simulation Type** : NVT equilibration - **Command Used for Simulation** : gmx mdrun -deffnm nvt - **MDP File Settings** : itle = FAS Charmm36 NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = sd ; Langevin dynamics integrator nsteps = 50000 ; 2 \* 50000 = 100 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 = shake ; shake algorithm constraints = h-bonds ; bonds involving H are constrained ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching 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) rvdw-switch = 1.2 ; Start switching at 12 Å vdw-modifier = Force-switch ; Enable switching function DispCorr = EnerPres ; account for cut-off vdW scheme ; 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 = no ; Temperature coupling is handled by the sd integrator tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau\_t = 1.0 1.0 ; time constant, in ps ref\_t = 300 300 ; 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 ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp = 300 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed ### Issue Description When I run the following command to extract the temperature: gmx energy -f nvt.edr -o temperature.xvg and select option `16` (Temperature), the output is: Temperature 301.807 – 0 0 (K) This shows that only one energy frame—at time 0.000 ps—was read, instead of the expected 101 frames over 100 ps. This suggests the simulation either didn’t progress beyond the initial step or the `nvt.edr` file wasn’t written correctly. ### Troubleshooting Steps Taken 1. **Checked Simulation Completion** : The `nvt.log` file ends at step 0, indicating the simulation didn’t proceed beyond the initial step. 2. **Inspected Energy File** : The `gmx energy` output confirms that `nvt.edr` contains only one frame, consistent with the log. 3. **Reviewed MDP Settings** : Verified that `nstenergy = 500` should save energies every 1 ps, which seems correct for a 100 ps run. 4. **Attempted to Visualize Trajectory** : I tried opening `nvt.trr` in Chimera and PyMOL, but got an error: I’d like your help with the following: 1. What could cause the simulation to stop at step 0? 2. Is the extremely negative pressure (-5,101.99 bar) a sign of an unstable initial configuration, and how can I fix this? 3. Are there specific settings in the MDP file I should check or adjust to ensure the simulation runs properly? Thank you so much for your time and assistance—I’m eager to get this simulation running smoothly! ---
**Author:** ![Gustavo](https://avatars.discourse-cdn.com/v4/letter/g/a9adbd/32.png) [@Gustavo](https://gromacs.bioexcel.eu/u/Gustavo)\ **Post date:** [March 31, 2025, 1:03pm UTC](https://gromacs.bioexcel.eu/t/issue-with-gromacs-simulation-mdp-file-parameters-and-nvt-equilibration/11840/2 "2025-03-31T13:03:32Z")
hi! try with this option: tcoupl=berendsen (for NVT equilibration) or tcoupl=nose-hoover (for NVT production). ---
**Author:** ![pritam\_biotech](https://avatars.discourse-cdn.com/v4/letter/p/919ad9/32.png) [@pritam\_biotech](https://gromacs.bioexcel.eu/u/pritam_biotech)\ **Post date:** [March 31, 2025, 3:21pm UTC](https://gromacs.bioexcel.eu/t/issue-with-gromacs-simulation-mdp-file-parameters-and-nvt-equilibration/11840/3 "2025-03-31T15:21:08Z")
As I am using sd integrator, is it necessary to add a separate thermostat? ---
**Author:** ![Gustavo](https://avatars.discourse-cdn.com/v4/letter/g/a9adbd/32.png) [@Gustavo](https://gromacs.bioexcel.eu/u/Gustavo)\ **Post date:** [March 31, 2025, 3:24pm UTC](https://gromacs.bioexcel.eu/t/issue-with-gromacs-simulation-mdp-file-parameters-and-nvt-equilibration/11840/4 "2025-03-31T15:24:41Z")
yes. The sd integrator is the way it is solving the equations of motion. The tcoupl is the way the ensemble (in this case NVT) is coupling the temperature. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [March 31, 2025, 3:29pm UTC](https://gromacs.bioexcel.eu/t/issue-with-gromacs-simulation-mdp-file-parameters-and-nvt-equilibration/11840/5 "2025-03-31T15:29:00Z")
Hi @pritam_biotech Are you sure the simulation produced any output? How large are the `.trr` and `.edr` files? It might be that the simulation never started and you only printed the first frame. Given that the log file also reports only step 0, I am pretty sure this was the case. Also regarding the `.trr` I suggest you to open it with VMD or to convert the `.trr` in an `.xtc` which should be handled correctly by Pymol. The mdp seems okay to me. The only thing is that you are really printing a ton, and you are printing positions/velocities/forces which will end up in a huge chunky file. Do you really need all this data? The [manual](https://manual.gromacs.org/current/user-guide/mdp-options.html#mdp-value-integrator-sd) states that `tcoupl` entry is ignored when using the `sd` integrator, so the thermostat entry will not be considered anyway.