GROMACS version:2021
GROMACS modification: Yes/No
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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
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.
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!
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.
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.
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.
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!