GROMACS version: 2021
GROMACS modification: No
Hi GROMACS users
I recently constructed a POPC lipid bilayer using CHARMM-GUI and my intention was to run it using GROMACS and Amber’s lipid17 force field.
However, it appears that the total charge of each lipid molecule is not an integer. It is close to zero but not exactly zero (see the itp file content from CHARMMM-GUI below).
I didn’t change any of the CHARMM-GUI output files, and I also checked in other resources that the atom charges provided by CHARMM-GUI are correct.
Obviously, I got the following warning from grompp:
NOTE 1 [file topol.top, line 28]:
System has non-zero total charge: -0.000612
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.
WARNING 1 [file topol.top, line 28]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
Did anyone encounter this problem before?
Any suggestions what to do?
POPC.itp
;; Generated by CHARMM-GUI FF-Converter
;;
;; Correspondance:
;; jul316@lehigh.edu or wonpil@lehigh.edu
;;
;; GROMACS topology file for POPC
;;
[ moleculetype ]
; name nrexcl
POPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 cD 1 PA C116 1 -0.125447 12.0100 ; qtot -0.125
2 hL 1 PA H16R 2 0.029046 1.0080 ; qtot -0.096
3 hL 1 PA H16S 3 0.029046 1.0080 ; qtot -0.067
4 hL 1 PA H16T 4 0.029046 1.0080 ; qtot -0.038
5 cD 1 PA C115 5 0.013975 12.0100 ; qtot -0.024
6 hL 1 PA H15R 6 0.009292 1.0080 ; qtot -0.015
7 hL 1 PA H15S 7 0.009292 1.0080 ; qtot -0.006
8 cD 1 PA C114 8 -0.020086 12.0100 ; qtot -0.026
9 hL 1 PA H14R 9 0.015929 1.0080 ; qtot -0.010
10 hL 1 PA H14S 10 0.015929 1.0080 ; qtot 0.006
11 cD 1 PA C113 11 -0.033096 12.0100 ; qtot -0.027
12 hL 1 PA H13R 12 0.014621 1.0080 ; qtot -0.012
13 hL 1 PA H13S 13 0.014621 1.0080 ; qtot 0.002
14 cD 1 PA C112 14 -0.027633 12.0100 ; qtot -0.025
15 hL 1 PA H12R 15 0.011368 1.0080 ; qtot -0.014
16 hL 1 PA H12S 16 0.011368 1.0080 ; qtot -0.003
17 cD 1 PA C111 17 -0.025206 12.0100 ; qtot -0.028
18 hL 1 PA H11R 18 0.014334 1.0080 ; qtot -0.014
19 hL 1 PA H11S 19 0.014334 1.0080 ; qtot 0.001
20 cD 1 PA C110 20 -0.028831 12.0100 ; qtot -0.028
21 hL 1 PA H10R 21 0.014691 1.0080 ; qtot -0.013
22 hL 1 PA H10S 22 0.014691 1.0080 ; qtot 0.001
23 cD 1 PA C19 23 -0.030472 12.0100 ; qtot -0.029
24 hL 1 PA H9R 24 0.013897 1.0080 ; qtot -0.015
25 hL 1 PA H9S 25 0.013897 1.0080 ; qtot -0.001
26 cD 1 PA C18 26 -0.015793 12.0100 ; qtot -0.017
27 hL 1 PA H8R 27 0.009067 1.0080 ; qtot -0.008
28 hL 1 PA H8S 28 0.009067 1.0080 ; qtot 0.001
29 cD 1 PA C17 29 -0.019630 12.0100 ; qtot -0.019
30 hL 1 PA H7R 30 0.011041 1.0080 ; qtot -0.008
31 hL 1 PA H7S 31 0.011041 1.0080 ; qtot 0.003
32 cD 1 PA C16 32 -0.024427 12.0100 ; qtot -0.021
33 hL 1 PA H6R 33 0.013334 1.0080 ; qtot -0.008
34 hL 1 PA H6S 34 0.013334 1.0080 ; qtot 0.006
35 cD 1 PA C15 35 -0.029387 12.0100 ; qtot -0.024
36 hL 1 PA H5R 36 0.016763 1.0080 ; qtot -0.007
37 hL 1 PA H5S 37 0.016763 1.0080 ; qtot 0.010
38 cD 1 PA C14 38 -0.030099 12.0100 ; qtot -0.020
39 hL 1 PA H4R 39 0.020877 1.0080 ; qtot 0.001
40 hL 1 PA H4S 40 0.020877 1.0080 ; qtot 0.021
41 cD 1 PA C13 41 -0.004882 12.0100 ; qtot 0.017
42 hL 1 PA H3R 42 0.019007 1.0080 ; qtot 0.036
43 hL 1 PA H3S 43 0.019007 1.0080 ; qtot 0.055
44 cD 1 PA C12 44 -0.149259 12.0100 ; qtot -0.095
45 hL 1 PA H2R 45 0.047345 1.0080 ; qtot -0.047
46 hL 1 PA H2S 46 0.047345 1.0080 ; qtot -0.000
47 cC 1 PC C11 47 0.798859 12.0100 ; qtot 0.799
48 oC 1 PC O12 48 -0.627537 16.0000 ; qtot 0.171
49 oS 1 PC O11 49 -0.424905 16.0000 ; qtot -0.254
50 cA 1 PC C1 50 -0.002091 12.0100 ; qtot -0.256
51 hE 1 PC HR 51 0.119283 1.0080 ; qtot -0.136
52 hE 1 PC HS 52 0.119283 1.0080 ; qtot -0.017
53 cA 1 PC C2 53 0.081076 12.0100 ; qtot 0.064
54 hE 1 PC HX 54 0.131246 1.0080 ; qtot 0.195
55 cA 1 PC C3 55 0.095565 12.0100 ; qtot 0.291
56 hE 1 PC HA 56 0.069089 1.0080 ; qtot 0.360
57 hE 1 PC HB 57 0.069089 1.0080 ; qtot 0.429
58 oT 1 PC O31 58 -0.445682 16.0000 ; qtot -0.017
59 pA 1 PC P31 59 1.076564 30.9700 ; qtot 1.060
60 oT 1 PC O32 60 -0.445682 16.0000 ; qtot 0.614
61 cA 1 PC C31 61 0.363063 12.0100 ; qtot 0.977
62 hE 1 PC H1A 62 0.013458 1.0080 ; qtot 0.991
63 hE 1 PC H1B 63 0.013458 1.0080 ; qtot 1.004
64 cA 1 PC C32 64 -0.282326 12.0100 ; qtot 0.722
65 hX 1 PC H2A 65 0.164858 1.0080 ; qtot 0.887
66 hX 1 PC H2B 66 0.164858 1.0080 ; qtot 1.052
67 nA 1 PC N31 67 0.198554 14.0100 ; qtot 1.250
68 cA 1 PC C33 68 -0.395982 12.0100 ; qtot 0.854
69 hX 1 PC H3A 69 0.194775 1.0080 ; qtot 1.049
70 hX 1 PC H3B 70 0.194775 1.0080 ; qtot 1.244
71 hX 1 PC H3C 71 0.194775 1.0080 ; qtot 1.438
72 cA 1 PC C34 72 -0.395982 12.0100 ; qtot 1.042
73 hX 1 PC H4A 73 0.194775 1.0080 ; qtot 1.237
74 hX 1 PC H4B 74 0.194775 1.0080 ; qtot 1.432
75 hX 1 PC H4C 75 0.194775 1.0080 ; qtot 1.627
76 cA 1 PC C35 76 -0.395982 12.0100 ; qtot 1.231
77 hX 1 PC H5A 77 0.194775 1.0080 ; qtot 1.426
78 hX 1 PC H5B 78 0.194775 1.0080 ; qtot 1.620
79 hX 1 PC H5C 79 0.194775 1.0080 ; qtot 1.815
80 oP 1 PC O33 80 -0.793092 16.0000 ; qtot 1.022
81 oP 1 PC O34 81 -0.793092 16.0000 ; qtot 0.229
82 oS 1 PC O21 82 -0.390929 16.0000 ; qtot -0.162
83 cC 1 PC C21 83 0.787558 12.0100 ; qtot 0.626
84 oC 1 PC O22 84 -0.625551 16.0000 ; qtot -0.000
85 cD 1 OL C12 85 -0.143418 12.0100 ; qtot -0.143
86 hL 1 OL H2R 86 0.042860 1.0080 ; qtot -0.101
87 hL 1 OL H2S 87 0.042860 1.0080 ; qtot -0.058
88 cD 1 OL C13 88 0.001619 12.0100 ; qtot -0.056
89 hL 1 OL H3R 89 0.019529 1.0080 ; qtot -0.037
90 hL 1 OL H3S 90 0.019529 1.0080 ; qtot -0.017
91 cD 1 OL C14 91 -0.022960 12.0100 ; qtot -0.040
92 hL 1 OL H4R 92 0.018134 1.0080 ; qtot -0.022
93 hL 1 OL H4S 93 0.018134 1.0080 ; qtot -0.004
94 cD 1 OL C15 94 -0.016692 12.0100 ; qtot -0.020
95 hL 1 OL H5R 95 0.008690 1.0080 ; qtot -0.012
96 hL 1 OL H5S 96 0.008690 1.0080 ; qtot -0.003
97 cD 1 OL C16 97 -0.023789 12.0100 ; qtot -0.027
98 hL 1 OL H6R 98 0.009266 1.0080 ; qtot -0.018
99 hL 1 OL H6S 99 0.009266 1.0080 ; qtot -0.008
100 cD 1 OL C17 100 -0.017495 12.0100 ; qtot -0.026
101 hL 1 OL H7R 101 0.019598 1.0080 ; qtot -0.006
102 hL 1 OL H7S 102 0.019598 1.0080 ; qtot 0.013
103 cD 1 OL C18 103 0.031775 12.0100 ; qtot 0.045
104 hL 1 OL H8R 104 0.032685 1.0080 ; qtot 0.078
105 hL 1 OL H8S 105 0.032685 1.0080 ; qtot 0.111
106 cB 1 OL C19 106 -0.244228 12.0100 ; qtot -0.134
107 hB 1 OL H9R 107 0.131512 1.0080 ; qtot -0.002
108 cB 1 OL C110 108 -0.239284 12.0100 ; qtot -0.241
109 hB 1 OL H10R 109 0.126878 1.0080 ; qtot -0.115
110 cD 1 OL C111 110 0.029059 12.0100 ; qtot -0.085
111 hL 1 OL H11R 111 0.033531 1.0080 ; qtot -0.052
112 hL 1 OL H11S 112 0.033531 1.0080 ; qtot -0.018
113 cD 1 OL C112 113 -0.026353 12.0100 ; qtot -0.045
114 hL 1 OL H12R 114 0.019717 1.0080 ; qtot -0.025
115 hL 1 OL H12S 115 0.019717 1.0080 ; qtot -0.005
116 cD 1 OL C113 116 -0.018257 12.0100 ; qtot -0.024
117 hL 1 OL H13R 117 0.013800 1.0080 ; qtot -0.010
118 hL 1 OL H13S 118 0.013800 1.0080 ; qtot 0.004
119 cD 1 OL C114 119 -0.024849 12.0100 ; qtot -0.021
120 hL 1 OL H14R 120 0.008572 1.0080 ; qtot -0.012
121 hL 1 OL H14S 121 0.008572 1.0080 ; qtot -0.004
122 cD 1 OL C115 122 -0.023247 12.0100 ; qtot -0.027
123 hL 1 OL H15R 123 0.010403 1.0080 ; qtot -0.017
124 hL 1 OL H15S 124 0.010403 1.0080 ; qtot -0.006
125 cD 1 OL C116 125 -0.012488 12.0100 ; qtot -0.019
126 hL 1 OL H16R 126 0.013659 1.0080 ; qtot -0.005
127 hL 1 OL H16S 127 0.013659 1.0080 ; qtot 0.009
128 cD 1 OL C117 128 0.008684 12.0100 ; qtot 0.017
129 hL 1 OL H17R 129 0.010026 1.0080 ; qtot 0.027
130 hL 1 OL H17S 130 0.010026 1.0080 ; qtot 0.037
131 cD 1 OL C118 131 -0.117290 12.0100 ; qtot -0.080
132 hL 1 OL H18R 132 0.026627 1.0080 ; qtot -0.053
133 hL 1 OL H18S 133 0.026627 1.0080 ; qtot -0.027
134 hL 1 OL H18T 134 0.026627 1.0080 ; qtot -0.000
Cheers,
Gal.