GROMACS version:2020.4
GROMACS modification: No
Here post your question:
GROMACS: gmx distance, version 2020.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /ricardo2/ricardo/lab_alunos/veronica/tipi_files/gromacs_files/tipi-wt_HNE/tutorial_umbrella
Command line:
gmx distance -s tipi-wt_HNE_pullc.tpr -f tipi-wt_HNE_pull_conf0.gro -select ‘com of group “Chain_E” plus com of group “Chain_I”’ -n index.ndx -oall tipi-wt_HNE_dist0.xvg
Reading file tipi-wt_HNE_pullc.tpr, VERSION 2020.4 (single precision)
Reading file tipi-wt_HNE_pullc.tpr, VERSION 2020.4 (single precision)
Program: gmx distance, version 2020.4
Source file: src/gromacs/selection/selectioncollection.cpp (line 614)
Function: void gmx::SelectionCollection::setTopology(gmx_mtop_t*, int)
Inconsistency in user input:
Invalid index group references encountered
Group ‘Chain_E’ cannot be used in selections, because it contains negative
atom indices and/or references atoms not present (largest allowed atom index
is 1010).
Group ‘Chain_I’ cannot be used in selections, because it contains negative
atom indices and/or references atoms not present (largest allowed atom index
is 1010).
Hi,
it looks like that index file and gro file are not compatible. You can re-generate the index file using gmx make_ndx and giving as input the gro tipi-wt_HNE_pull_conf0.gro.
Best regards
Alessandra
Hi, Alessandra.
Thanks for your help, but I loose this works and start another but now I’m not able to reproduce the last one.
Now I have the follow problem:
Command line:
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘optimize_fft’
Ignoring obsolete mdp entry ‘ns_type’
Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’
Setting the LD random seed to 1461744737
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 3 bonded neighbours molecule type ‘Protein_chain_E’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_I’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘NA’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘CL’
turning H bonds into constraints…
WARNING 1 [file topol.top, line 50]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
POSRES_B
If you haven’t made a spelling error, either use the macro you defined,
or don’t define the macro
Pull group 1 ‘Chain_E’ has 3565 atoms
Pull group 2 ‘Chain_I’ has 860 atoms
Number of degrees of freedom in T-Coupling group Protein is 9552.59
Number of degrees of freedom in T-Coupling group non-Protein is 60159.41
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.493 nm, buffer size 0.093 nm
Set rlist, assuming 4x4 atom pair-list, to 1.418 nm, buffer size 0.018 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 100.000
Using frame at t = 100 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 56x40x100, spacing 0.117 0.109 0.120
Pull group natoms pbc atom distance at start reference at t=0
1 3565 1783
2 860 3389 0.218 nm 0.218 nm
Estimate for the relative computational load of the PME mesh part: 0.13
This run will generate roughly 319 Mb of data
There was 1 warning
Program: gmx grompp, version 2020.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option
Please, can you help again
thanks in advance
Ricardo
Hi,
The 'define" option in mdp does not match with the provided input files. Look what is associated to the option ‘define’ in your mdp file and check that definition is also giving in the topology file
more define option in Molecular dynamics parameters (.mdp options) — GROMACS 2020.5 documentation
In general, it is good praxis to create a new topic for each new problem or questions, such as the title match with the problem and facilitate the answer of other users.
Best regards
Alessandra