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How to check the "PULL EFIELD" command is applied ?
#37712 11/20/19 09:54 AM
Joined: Aug 2019
Posts: 14
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sohyeon Offline OP
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Joined: Aug 2019
Posts: 14
Deal all

I used "pull efield" command to apply e-field force. But the energy of EPOLAR and PULL are zero until 3 ns of NVT in the output file.

Is it not applied correctly or is normal situation?

Pleas help me. Thank you.


1. ##This is my script ##
! Read topology and parameter files
stream toppar.str
stream input.prm

calc num0 = @num - 1
! Read PSF and Coordinates
open read unit 10 card name ../../../../3.pbc/step3_pbcsetup.psf
read psf unit 10 card
if num .eq. 0 then
open read unit 10 card name ../../../../3.pbc/step3_pbcsetup.crd
endif
if num .ne. 0 then
open read unit 10 card name 4.@{num0}.crd
endif
read coor unit 10 card

!
! Setup PBC (Periodic Boundary Condition)
!

stream ../../../../3.pbc/step3_pbcsetup.str

open read unit 10 card name ../../../../3.pbc/crystal_image.str
CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma
CRYSTAL READ UNIT 10 CARD

!Image centering by residue
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele segid @MOLNAME end
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele segid @METAL end
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele segid @CNAME end

!
! Efield - +1V
!
if EV .gt. 0 then
pull efield 1 zdir 1.0 sele resi 1:30 .and. resn BIPY end
pull list
pull efield @EV zdir 1.0 sele resi 1:160 .and. resn AGM end
pull efield @EV zdir -1.0 sele resi 31:60 .and. resn BIPY end
pull efield @EV zdir -1.0 sele resi 241:400 .and. resn AGM end
endif





2. ##pull command part of output##
CHARMM> !
CHARMM> ! Efield - +1V
CHARMM> !
CHARMM> if EV .gt. 0 then
Comparing "1" and "0".
IF test evaluated as true. Performing command

CHARMM> pull efield 1 zdir 1.0 sele resi 1:3 .and. resn BIPY end
SELRPN> 168 atoms have been selected out of 3760

PULL> 168 pulling force(s) added. Total now 168


CHARMM> pull list
PULL> Currently these 168 external forces are defined
Atom Ampl [AKMA] [pN] Swit Start[pN] Per [ps] Direction (X,Y,Z)
1 BIPY 1 BIPY C1 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
2 BIPY 1 BIPY C2 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
3 BIPY 1 BIPY C3 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
4 BIPY 1 BIPY C4 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
5 BIPY 1 BIPY C5 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
6 BIPY 1 BIPY N6 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
7 BIPY 1 BIPY H7 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
8 BIPY 1 BIPY H8 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
9 BIPY 1 BIPY H9 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
10 BIPY 1 BIPY C10 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
11 BIPY 1 BIPY C11 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
12 BIPY 1 BIPY N12 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
13 BIPY 1 BIPY C13 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
14 BIPY 1 BIPY H14 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
15 BIPY 1 BIPY C15 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
16 BIPY 1 BIPY C16 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
17 BIPY 1 BIPY H17 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
18 BIPY 1 BIPY H18 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
19 BIPY 1 BIPY C19 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
20 BIPY 1 BIPY H20 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
21 BIPY 1 BIPY H21 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
22 BIPY 1 BIPY H22 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
23 BIPY 1 BIPY C23 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
24 BIPY 1 BIPY H24 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
25 BIPY 1 BIPY H25 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
26 BIPY 1 BIPY C26 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
27 BIPY 1 BIPY H27 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
28 BIPY 1 BIPY H28 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
29 BIPY 1 BIPY C29 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
30 BIPY 1 BIPY H30 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
31 BIPY 1 BIPY H31 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
32 BIPY 1 BIPY C32 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
33 BIPY 1 BIPY H33 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
34 BIPY 1 BIPY H34 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
35 BIPY 1 BIPY C35 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
36 BIPY 1 BIPY H36 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
37 BIPY 1 BIPY H37 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
38 BIPY 1 BIPY C38 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
39 BIPY 1 BIPY H39 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
40 BIPY 1 BIPY H40 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
41 BIPY 1 BIPY C41 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
42 BIPY 1 BIPY H42 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
43 BIPY 1 BIPY H43 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
44 BIPY 1 BIPY C44 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
45 BIPY 1 BIPY H45 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
46 BIPY 1 BIPY H46 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
47 BIPY 1 BIPY C47 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
48 BIPY 1 BIPY H48 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
49 BIPY 1 BIPY H49 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
50 BIPY 1 BIPY C50 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
51 BIPY 1 BIPY H51 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
52 BIPY 1 BIPY H52 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
53 BIPY 1 BIPY C53 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
54 BIPY 1 BIPY H54 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
55 BIPY 1 BIPY H55 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
56 BIPY 1 BIPY S56 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
57 BIPY 2 BIPY C1 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
58 BIPY 2 BIPY C2 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
59 BIPY 2 BIPY C3 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
60 BIPY 2 BIPY C4 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
61 BIPY 2 BIPY C5 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
62 BIPY 2 BIPY N6 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
63 BIPY 2 BIPY H7 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
64 BIPY 2 BIPY H8 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
65 BIPY 2 BIPY H9 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
66 BIPY 2 BIPY C10 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
67 BIPY 2 BIPY C11 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
68 BIPY 2 BIPY N12 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
69 BIPY 2 BIPY C13 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
70 BIPY 2 BIPY H14 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
71 BIPY 2 BIPY C15 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
72 BIPY 2 BIPY C16 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
73 BIPY 2 BIPY H17 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
74 BIPY 2 BIPY H18 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
75 BIPY 2 BIPY C19 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
76 BIPY 2 BIPY H20 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
77 BIPY 2 BIPY H21 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
78 BIPY 2 BIPY H22 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
79 BIPY 2 BIPY C23 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
80 BIPY 2 BIPY H24 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
81 BIPY 2 BIPY H25 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
82 BIPY 2 BIPY C26 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
83 BIPY 2 BIPY H27 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
84 BIPY 2 BIPY H28 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
85 BIPY 2 BIPY C29 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
86 BIPY 2 BIPY H30 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
87 BIPY 2 BIPY H31 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
88 BIPY 2 BIPY C32 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
89 BIPY 2 BIPY H33 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
90 BIPY 2 BIPY H34 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
91 BIPY 2 BIPY C35 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
92 BIPY 2 BIPY H36 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
93 BIPY 2 BIPY H37 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
94 BIPY 2 BIPY C38 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
95 BIPY 2 BIPY H39 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
96 BIPY 2 BIPY H40 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
97 BIPY 2 BIPY C41 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
98 BIPY 2 BIPY H42 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
99 BIPY 2 BIPY H43 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
100 BIPY 2 BIPY C44 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
101 BIPY 2 BIPY H45 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
102 BIPY 2 BIPY H46 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
103 BIPY 2 BIPY C47 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
104 BIPY 2 BIPY H48 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
105 BIPY 2 BIPY H49 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
106 BIPY 2 BIPY C50 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
107 BIPY 2 BIPY H51 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
108 BIPY 2 BIPY H52 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
109 BIPY 2 BIPY C53 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
110 BIPY 2 BIPY H54 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
111 BIPY 2 BIPY H55 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
112 BIPY 2 BIPY S56 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
113 BIPY 3 BIPY C1 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
114 BIPY 3 BIPY C2 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
115 BIPY 3 BIPY C3 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
116 BIPY 3 BIPY C4 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
117 BIPY 3 BIPY C5 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
118 BIPY 3 BIPY N6 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
119 BIPY 3 BIPY H7 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
120 BIPY 3 BIPY H8 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
121 BIPY 3 BIPY H9 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
122 BIPY 3 BIPY C10 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
123 BIPY 3 BIPY C11 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
124 BIPY 3 BIPY N12 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
125 BIPY 3 BIPY C13 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
126 BIPY 3 BIPY H14 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
127 BIPY 3 BIPY C15 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
128 BIPY 3 BIPY C16 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
129 BIPY 3 BIPY H17 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
130 BIPY 3 BIPY H18 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
131 BIPY 3 BIPY C19 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
132 BIPY 3 BIPY H20 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
133 BIPY 3 BIPY H21 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
134 BIPY 3 BIPY H22 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
135 BIPY 3 BIPY C23 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
136 BIPY 3 BIPY H24 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
137 BIPY 3 BIPY H25 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
138 BIPY 3 BIPY C26 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
139 BIPY 3 BIPY H27 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
140 BIPY 3 BIPY H28 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
141 BIPY 3 BIPY C29 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
142 BIPY 3 BIPY H30 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
143 BIPY 3 BIPY H31 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
144 BIPY 3 BIPY C32 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
145 BIPY 3 BIPY H33 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
146 BIPY 3 BIPY H34 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
147 BIPY 3 BIPY C35 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
148 BIPY 3 BIPY H36 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
149 BIPY 3 BIPY H37 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
150 BIPY 3 BIPY C38 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
151 BIPY 3 BIPY H39 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
152 BIPY 3 BIPY H40 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
153 BIPY 3 BIPY C41 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
154 BIPY 3 BIPY H42 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
155 BIPY 3 BIPY H43 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
156 BIPY 3 BIPY C44 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
157 BIPY 3 BIPY H45 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
158 BIPY 3 BIPY H46 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
159 BIPY 3 BIPY C47 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
160 BIPY 3 BIPY H48 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
161 BIPY 3 BIPY H49 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
162 BIPY 3 BIPY C50 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
163 BIPY 3 BIPY H51 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
164 BIPY 3 BIPY H52 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
165 BIPY 3 BIPY C53 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00
166 BIPY 3 BIPY H54 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
167 BIPY 3 BIPY H55 0.0000 0.000 0 0.000 -1.000 0.00 0.00 1.00
168 BIPY 3 BIPY S56 -0.0000 -0.000 0 0.000 -1.000 0.00 0.00 1.00









3. ##Energy part of output##
DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
DYNA EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
DYNA POLAR: EPOLAR PULL
DYNA MMFP: GEO MDIP SSBP SHEL DROFfa
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
---------- --------- --------- --------- --------- ---------
DYNA> 0 0.00000 49762.28845 2082.85636 47679.43209 255.02214
DYNA PROP> 15.35281 49762.28845 0.00000 0.00000 3166.88804
DYNA INTERN> 947.43383 2149.62966 546.10988 1770.25262 0.00000
DYNA EXTERN> 596.66095 83.04289 0.00000 0.00000 0.00000
DYNA IMAGES> -430.11037 36.22118 0.00000 0.00000 0.00000
DYNA EWALD> 45519.73677 -9530.13659 4803.96538 0.00000 0.00000
DYNA POLAR> 0.00000 -0.00000
DYNA MMFP> 1186.62589 0.00000 0.00000 0.00000 0.00000
DYNA PRESS> -21523.53253 19412.27384 25828.98832 24961.73781 57138.56000
---------- --------- --------- --------- --------- -------



Last edited by sohyeon; 11/20/19 10:01 AM.
Re: How to check the "PULL EFIELD" command is applied ?
sohyeon #37713 11/20/19 12:29 PM
Joined: Sep 2003
Posts: 4,794
Likes: 2
Forum Member
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Forum Member
Joined: Sep 2003
Posts: 4,794
Likes: 2
The unit for the electric field is V/m in the pull command. 1 V/m is a very low field strength in this context. See the testcase
c25test/pull.inp


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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