Mismatch between index file and tpr log

User discussions
1

GROMACS version:2023
GROMACS modification: No

I have prepared an index file to be used in pull code . As i defined in make_ndex command there are 21 k atoms in one group and 12 k atoms in the 2nd group. but when i run grompp to generate tpr file, i can see in command line window that gmx lists 21 k for the first group but 6k atoms for the 2nd group. i rechecked my index file and it seems ok . i do not know what is wrong and how could i fix this mismatch. can anybody hint to any resolution? part of mdp file including pull code follows:

pull = yes ;
pull-coord1-type = umbrella ;
pull-coord1-geometry = distance ;
pull-ngroups = 2 ;
pull-ncoords = 1 ;
pull-coord1-dim = N Y N;
pull-group1-name = beta ;
pull-group2-name = gama ;
pull-coord1-groups = 1 2 ;
pull-coord1-rate = 0.0 ; ;
pull-coord1-start = yes ;
pull-coord1-k = 5000;
pull-nstxout = 2000;
pull-nstfout = 2000;

2

Hi,

can anyone offer any help to resolve this issue? i have repeated the step and still the mismatch remains unresolved.

3

Can you please provide the full terminal output from grompp and what gmx check reports for the contents of the index file?

4

here is the grompp terminal output :

Blockquote Command line:
gmx grompp -f eq.mdp -c step4.gro -r step4.gro -p topol.top -n index2.ndx -o eq.tpr

Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’
Generated 1827 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 780 of the 1830 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘PAA1’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘PAD1’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘PAG1’

turning H bonds into constraints…

Excluding 1 bonded neighbours molecule type ‘SOD’

turning H bonds into constraints…

Setting gen_seed to -1342179330

Velocities were taken from a Maxwell distribution at 310 K
Pull group 1 ‘beta’ has 21254 atoms
Pull group 2 ‘gama’ has 6206 atoms
Number of degrees of freedom in T-Coupling group Protein is 81621.00
Number of degrees of freedom in T-Coupling group non-Protein is 2943.00

The largest distance between excluded atoms is 0.598 nm between atom 21225 and 21234

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K

Calculated rlist for 1x1 atom pair-list as 2.188 nm, buffer size 0.988 nm

Set rlist, assuming 4x4 atom pair-list, to 1.889 nm, buffer size 0.689 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

NOTE 1 [file eq.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 120x120x120, spacing 0.500 0.500 0.500
Pull group natoms pbc atom distance at start reference at t=0
1 21254 10627
2 6206 24357 5.505 nm 5.505 nm

Estimate for the relative computational load of the PME mesh part: 0.73

NOTE 2 [file eq.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 70 Mb of data

There were 2 NOTEs

and the content of gmx check :

Blockquote gmx check -n index2.ndx

Contents of index file index2.ndx

Nr. Group #Entries First Last
0 System 33684 1 33684
1 Protein 32522 1 33094
2 Protein-H 16580 1 33094
3 C-alpha 2070 5 33077
4 Backbone 6210 1 33092
5 MainChain 8268 1 33092
6 MainChain+Cb 10178 1 33092
7 MainChain+H 10252 1 33092
8 SideChain 22270 2 33094
9 SideChain-H 8312 7 33094
10 Prot-Masses 32522 1 33094
11 non-Protein 1162 10342 33684
12 Other 1162 10342 33684
13 AGLCN 432 10342 33608
14 BMAN 80 10396 33454
15 AMAN 168 10416 33581
16 AGAL 84 10464 33523
17 ANE5A 296 10485 33666
18 BGAL 84 10570 33629
19 SOD 18 33667 33684
20 beta 21254 1 21254
21 gama 6206 21255 33666

please note the mismatch between nr of atoms in group 21 (gama) and the index of the first & last atoms in the same.

5

There is no mismatch. grompp and gmx check are telling you the exact same thing. The “gama” group has 6206 atoms, but what’s shown does not mean it is continuous from atom 21255 to atom 33666. It contains about half the atoms in that range. Double check how you are generating it, because it sounds like it does not contain what you think it does.