# Error in NPT **URL:** \ **Category:** User discussions\ **Tags:** grompp, topology\ **Created:** [November 8, 2023, 9:10am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575 "2023-11-08T09:10:30Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![zhangjie](https://avatars.discourse-cdn.com/v4/letter/z/858c86/32.png) [@zhangjie](https://gromacs.bioexcel.eu/u/zhangjie)\ **Post date:** [November 8, 2023, 9:10am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/1 "2023-11-08T09:10:30Z")
GROMACS version:2021 GROMACS modification: Yes/No Here post your question Dear user： I don’t Know how to solve this problem Error in user input: Invalid input values In option s Required option was not provided, and the default file ‘topol’ does not exist or is not accessible. The following extensions were tried to complete the file name: .tpr ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [November 8, 2023, 9:48am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/2 "2023-11-08T09:48:13Z")
`gmx mdrun` cannot find your input file (tpr file). It says there’s no topol.tpr (default file name) in the directory you are starting from. If the file is called something else you need to specify that with the `-s` option. ---
**Author:** ![zhangjie](https://avatars.discourse-cdn.com/v4/letter/z/858c86/32.png) [@zhangjie](https://gromacs.bioexcel.eu/u/zhangjie)\ **Post date:** [November 8, 2023, 10:58am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/3 "2023-11-08T10:58:14Z")
Thank you for your answer! There was no tpr file generated after running **“gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr”**. In fact, an error occured as follows: ######## NOTE 2 [file npt.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. ## This run will generate roughly 30 Mb of data There were 2 notes1 There was 1 warning Program: gmx grompp, version 2021.5 Source file: src\gromacs\gmxpreprocess\grompp.cpp (line 2389) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. ######### How can get the tpr file? Thank you for your kind heart again! ---
**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 8, 2023, 2:29pm UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/4 "2023-11-08T14:29:13Z")
There will be a WARNING printed above. Notes are informational, warnings tell you there is a problem. You need to fix whatever the warning is complaining about, and if you need help with that, please provide the full terminal output from `grompp`. ---
**Author:** ![zhangjie](https://avatars.discourse-cdn.com/v4/letter/z/858c86/32.png) [@zhangjie](https://gromacs.bioexcel.eu/u/zhangjie)\ **Post date:** [November 9, 2023, 2:03am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/5 "2023-11-09T02:03:49Z")
**Thank you for you answer! I** **I have created a box containing 500 tip4p water molecules. I would like to simulate the freezing procedure.** The warnings generated after running grompp are as follows: NOTE 1 [file npt.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Setting the LD random seed to -1570249794 Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 2 bonded neighbours molecule type ‘SOL’ turning H bonds into constraints… Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 500 Water residues WARNING 1 [file npt.mdp]: For proper integration of the Nose-Hoover thermostat, tau-t (0.1) should be at least 20 times larger than nsttcouple\*dt (0.02) Number of degrees of freedom in T-Coupling group System is 2997.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 600.000 Using frame at t = 600 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.143 0.143 0.143 Estimate for the relative computational load of the PME mesh part: 0.82 NOTE 2 [file npt.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. ---
**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 9, 2023, 4:23am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/6 "2023-11-09T04:23:37Z")
> [@zhangjie](#): > > WARNING 1 [file npt.mdp]: > For proper integration of the Nose-Hoover thermostat, tau-t (0.1) should > be at least 20 times larger than nsttcouple\*dt (0.02) The warning tells you your minimum `tau-t` value should be 0.4; using 0.1 is much too tight of coupling. Typical values would be on the order of 0.5-1.0 or so. ---
**Author:** ![zhangjie](https://avatars.discourse-cdn.com/v4/letter/z/858c86/32.png) [@zhangjie](https://gromacs.bioexcel.eu/u/zhangjie)\ **Post date:** [November 9, 2023, 6:45am UTC](https://gromacs.bioexcel.eu/t/error-in-npt/7575/7 "2023-11-09T06:45:23Z")
Thank you for your kind heart again! I changed “tau-t”. In addition, I found I didn’t run “make\_ndx” so that I have no index.ndx file. After prepared aboved things, I can run my model now!