GROMACS version: 2019.6
GROMACS modification: No
I am running a coarse-grained simulation, and I am seeing the following note:
NOTE 4 [file topol.top, line 75]:
In moleculetype ‘PNM’ 40 atoms are not bound by a potential or constraint
to any other atom in the same moleculetype. Although technically this
might not cause issues in a simulation, this often means that the user
forgot to add a bond/potential/constraint or put multiple molecules in
the same moleculetype definition by mistake. Run with -v to get
information for each atom.
I don’t understand why I am seeing this note. I am running a custom linear polymer simulation with the terminal beads being a certain type (TTA, TTB), and every nonterminal bead is the same type.
This is my topol.top file:
#define _FF_GROMACS
#define _FF_GROMACS1
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
[ atomtypes ]
;type mass charge ptype sigma epsilon
TTA 114 0.000 A 0.000 1.000
TTB 114 0.000 A 0.000 1.000
TM 113 0.000 A 0.000 1.000
TW 18.010 0.000 A 0.000 1.0000
[ moleculetype ]
;name nrexcel
PNM 3
[ atoms ]
; nr atoms resnr residue atom cgnr charge mass typeB chargeB massB
1 TTA 1 PNM BTA 1 0.000
2 TM 2 PNM BM2 2 0.000
3 TM 3 PNM BM3 3 0.000
4 TM 4 PNM BM4 4 0.000
5 TM 5 PNM BM5 5 0.000
6 TM 6 PNM BM6 6 0.000
7 TM 7 PNM BM7 7 0.000
8 TM 8 PNM BM8 8 0.000
9 TM 9 PNM BM9 9 0.000
10 TM 10 PNM BM10 10 0.000
11 TM 11 PNM BM11 11 0.000
12 TM 12 PNM BM12 12 0.000
13 TM 13 PNM BM13 13 0.000
14 TM 14 PNM BM14 14 0.000
15 TM 15 PNM BM15 15 0.000
16 TM 16 PNM BM16 16 0.000
17 TM 17 PNM BM17 17 0.000
18 TM 18 PNM BM18 18 0.000
19 TM 19 PNM BM19 19 0.000
20 TM 20 PNM BM20 20 0.000
21 TM 21 PNM BM21 21 0.000
22 TM 22 PNM BM22 22 0.000
23 TM 23 PNM BM23 23 0.000
24 TM 24 PNM BM24 24 0.000
25 TM 25 PNM BM25 25 0.000
26 TM 26 PNM BM26 26 0.000
27 TM 27 PNM BM27 27 0.000
28 TM 28 PNM BM28 28 0.000
29 TM 29 PNM BM29 29 0.000
30 TM 30 PNM BM30 30 0.000
31 TM 31 PNM BM31 31 0.000
32 TM 32 PNM BM32 32 0.000
33 TM 33 PNM BM33 33 0.000
34 TM 34 PNM BM34 34 0.000
35 TM 35 PNM BM35 35 0.000
36 TM 36 PNM BM36 36 0.000
37 TM 37 PNM BM37 37 0.000
38 TM 38 PNM BM38 38 0.000
39 TM 39 PNM BM39 39 0.000
40 TTB 40 PNM BTB 40 0.000
[ bonds ]
;
1 2 1 0.5 100000
2 3 1 0.5 100000
3 4 1 0.5 100000
4 5 1 0.5 100000
5 6 1 0.5 100000
6 7 1 0.5 100000
7 8 1 0.5 100000
8 9 1 0.5 100000
9 10 1 0.5 100000
10 11 1 0.5 100000
11 12 1 0.5 100000
12 13 1 0.5 100000
13 14 1 0.5 100000
14 15 1 0.5 100000
15 16 1 0.5 100000
16 17 1 0.5 100000
17 18 1 0.5 100000
18 19 1 0.5 100000
19 20 1 0.5 100000
20 21 1 0.5 100000
21 22 1 0.5 100000
22 23 1 0.5 100000
23 24 1 0.5 100000
24 25 1 0.5 100000
25 26 1 0.5 100000
26 27 1 0.5 100000
27 28 1 0.5 100000
28 29 1 0.5 100000
29 30 1 0.5 100000
30 31 1 0.5 100000
31 32 1 0.5 100000
32 33 1 0.5 100000
33 34 1 0.5 100000
34 35 1 0.5 100000
35 36 1 0.5 100000
36 37 1 0.5 100000
37 38 1 0.5 100000
38 39 1 0.5 100000
39 40 1 0.5 100000
[ moleculetype ]
;
SOL 1
[ atoms ]
;
1 TW 1 SOL BW 1 0.0000
[ system ]
40nipam-in-water
[ molecules ]
;compound # mol
PNM 1
SOL 10994
I have provided bond constraints to my atoms, but apparently that does not suffice? Any advice would be appreciated.