-
Notifications
You must be signed in to change notification settings - Fork 1
/
dyna41315.txt~
89 lines (70 loc) · 2.66 KB
/
dyna41315.txt~
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
* cel48F + bglc + tip3
*
resize chsize 500000
bomblev 0
wrnlev 2
open unit 12 read form name top_all36_carb.rtf !/home/chen/para/newTOPPAR/
read rtf card unit 12
close unit 12
open unit 13 read form name par_all36_carb.prm !/home/chen/para/newTOPPAR/
read param card flex unit 13
close unit 13
open unit 10 read form name top_all22_prot.rtf !/home/chen/para/newtoppar/
read rtf card append unit 10
close unit 10
open unit 11 read form name par_all22_prot.prm !/home/chen/para/newtoppar/
read param card flex append unit 11
close unit 11
open unit 9 card name prot_sequence.txt
read sequence card unit 9
close unit 9
generate prot setup
open unit 14 card name bglc_sequence.txt
read sequence card unit 14
close unit 14
generate bglc setup
read sequence tips 20241
generate water noangle nodihedral setup
open unit 15 card name ion_sequence.txt
read sequence card unit 15
close unit 15
generate ions setup
open unit 16 card name sys_pore_wt.cor
read coor card unit 16
close unit 16
set dim 96.20
crystal define cubic @dim @dim @dim 90.0 90.0 90.0
crystal build cutoff 12.0 noper 0
!image byres sele resn TIP3 end
!image byseg sele segid PROT end
!image byres sele resn SOD end
!image byres sele resn BGLC end
shake fast bonH param
!!! production CPT !!!
!open unit 11 read form name celfsys-bglc-equ.rst
!open unit 12 write form name celfsys-bglc-dyn-1.rst
open unit 21 write unform name celfsys-bglc-dyn-1.dcd
open unit 22 write form name celfsys-bglc-dyn-1.mon
!Dynamics restart cpt timestep 0.001 nstep 500000 iseed 198401235 -
!FIRSTT 323.0 FinalT 323.0 TEMINC 0.0 -
!nprint 100 iprfrq 500 -
!pconstant PINTernal pmass 400.0 pref 1.0 pgamma 20.0 - !use extended system meth in P. !NB: pgamma should be 0.0
!tbath 323.0 tcons -
!HOOVer tmass 1000.0 reft 323.0 - ! use extended system meth in T
!EWALD PMEWALD KAPPA 0.32 FFTX 90 FFTY 90 FFTZ 90 ORDER 6 -
!BYCBim CUTNB 12.0 CTOFNB 10.0 CTONNB 9.0 cutim 12.0 -
!VDW VSWITCH NTRFRQ 10 -
!inbfrq -1 ihbfrq 0 imgfrq -1 - ! heuristic update
!iunread 11 iunwrit 12 iuncrd 21 kunit 22 nsavc 1000 ! nsavc is the frq of writing coords
dynamics cpt timestep 0.001 nstep 10 iseed 198401235 -
firstt 323.0 finalt 323.0 teminc 0.0 -
nprint 1 iprfrq 1 -
pconstant pinternal pmass 400.0 pref 1.0 pgamma 20.0 -
tbath 323.0 tcons -
hoover tmass 1000.0 reft 323.0 -
EWALD PMEWALD KAPPA 0.32 FFTX 90 FFTY 90 FFTZ 90 ORDER 6 -
BYCBim CUTNB 12.0 CTOFNB 10.0 CTONNB 9.0 -
VDW VSWITCH NTRFRQ 10 -
inbfrq -1 ihbfrq 0 imgfrq -1 - ! heuristic update
iuncrd 21 kunit 22 nsavc 1 ! nsavc is the frq of writing coords
stop