[gmx-users] free energy
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Sun Jan 3 18:24:06 CET 2010
Hey All,
I am trying to calculate the solvation free energy of glucose in ionic
liquids. I am getting really large value for lamda=0 in vacuum and
solvent as well. I am getting final solvation energy value ~ 310 kJ/mol.
Can you tell me where I am wrong.
Here I have pasted the the lamda value in vacuum and solvent
Vacuum Solvent
0.0 527.16 0.0 4284.769
0.1 74.119 0.1 161.606
0.2 37.9665 0.2 -16.3176
0.3 28.748 0.3 -52.488
0.4 7.555 0.4 -4.3341
0.5 1.495 0.5 6.996
0.6 -4.796 0.6 155.485
0.7 2.361 0.7 174.20
0.8 3.69 0.8 193.016
0.9 5.483 0.9 201.820
0.92 6.391 0.92 211.79
1.0 8.887 1.0 227.79
For each lamda value I equibrate the system for 1ns and run the dynamics
for 4 ns.
here is dynamics file I used. pasted the topology file at the end.
title = cpeptide MD
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.001 ; ps !
nsteps = 4000000 ; total 5 ps.
nstcomm = 1
nstxout = 50
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.4
coulombtype = PME
vdwtype = cut-off
pbc = xyz
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps =system
ref_t = 350
; Pressure coupling is on
Pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 350.0
gen_seed = 173529
free_energy = yes
init_lambda = 0.00
sc-alpha = 0.6
sc_power = 1
Thanks
Nilesh
Topology file (not pasted whole because of size)
;
; File 'glu-ac.top' was generated
; By user: ndhumal (36026)
; On host: c20
; At date: Tue Dec 15 15:25:07 2009
;
; This is your topology file
; Gromacs Runs One Microsecond At Cannonball Speeds
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_180 1 GUL O 1 -0.4 15.9994
opls_180 0.0 15.9994
2 opls_159 1 GUL C2 2 0.365 12.011
opls_159 0.0 12.011
3 opls_159 1 GUL C3 2 0.205 12.011
opls_159 0.0 12.011
4 opls_159 1 GUL C4 2 0.205 12.011
opls_159 0.0 12.011
5 opls_159 1 GUL C5 2 0.205 12.011
opls_159 0.0 12.011
6 opls_137 1 GUL C6 2 0.17 12.011
opls_137 0.0 12.011
7 opls_159 1 GUL C7 2 0.145 12.011
opls_159 0.0 12.011
8 opls_169 1 GUL O8 3 -0.7 15.9994
opls_169 0.0 15.9994
9 opls_169 1 GUL O9 3 -0.7 15.9994
opls_169 0.0 15.9994
10 opls_169 1 GUL O10 3 -0.7 15.9994
opls_169 0.0 15.9994
11 opls_169 1 GUL O11 3 -0.7 15.9994
opls_169 0.0 15.9994
12 opls_154 1 GUL O12 3 -0.683 15.9994
opls_154 0.0 15.9994
13 opls_140 1 GUL H13 4 0.1 1.008
opls_140 0.0 1.008
14 opls_140 1 GUL H14 4 0.06 1.008
opls_140 0.0 1.008
15 opls_140 1 GUL H15 4 0.06 1.008
opls_140 0.0 1.008
16 opls_140 1 GUL H16 4 0.06 1.008
opls_140 0.0 1.008
17 opls_140 1 GUL H17 4 0.03 1.008
opls_140 0.0 1.008
18 opls_155 1 GUL H18 5 0.435 1.008
opls_155 0.0 1.008
19 opls_155 1 GUL H19 5 0.435 1.008
opls_155 0.0 1.008
20 opls_155 1 GUL H20 5 0.435 1.008
opls_155 0.0 1.008
21 opls_155 1 GUL H21 5 0.435 1.008
opls_155 0.0 1.008
22 opls_140 1 GUL H22 5 0.06 1.008
opls_140 0.0 1.008
23 opls_140 1 GUL H23 5 0.06 1.008
opls_140 0.0 1.008
24 opls_155 1 GUL H24 6 0.418 1.008
opls_155 0.0 1.008
25 opls_561 2 EMI C 7 -0.13 12.011 ;
qtot -0.13
26 opls_561 2 EMI C2 8 -0.13 12.011 ;
qtot -0.26
27 opls_557 2 EMI N3 9 0.15 14.0067 ;
qtot -0.11
28 opls_558 2 EMI C4 10 -0.11 12.011 ;
qtot -0.22
29 opls_557 2 EMI N5 11 0.15 14.0067 ;
qtot -0.07
30 opls_135 2 EMI C6 12 -0.17 12.011 ;
qtot -0.24
31 opls_136 2 EMI C7 13 -0.05 12.011 ;
qtot -0.29
32 opls_135 2 EMI C8 14 -0.17 12.011 ;
qtot -0.46
33 opls_564 2 EMI H9 15 0.21 1.008 ;
qtot -0.25
34 opls_564 2 EMI H10 15 0.21 1.008 ;
qtot -0.04
35 opls_563 2 EMI H11 15 0.21 1.008 ;
qtot 0.17
36 opls_140 2 EMI H12 16 0.13 1.008 ;
qtot 0.3
37 opls_140 2 EMI H13 16 0.13 1.008 ;
qtot 0.43
38 opls_140 2 EMI H14 16 0.13 1.008 ;
qtot 0.56
39 opls_140 2 EMI H15 17 0.13 1.008 ;
qtot 0.69
40 opls_140 2 EMI H16 17 0.13 1.008 ;
qtot 0.82
41 opls_140 2 EMI H17 18 0.06 1.008 ;
qtot 0.88
42 opls_140 2 EMI H18 18 0.06 1.008 ;
qtot 0.94
43 opls_140 2 EMI H19 18 0.06 1.008 ;
qtot 1
44 opls_561 3 EMI C 19 -0.13 12.011 ;
qtot 0.87
45 opls_561 3 EMI C2 20 -0.13 12.011 ;
qtot 0.74
46 opls_557 3 EMI N3 21 0.15 14.0067 ;
qtot 0.89
47 opls_558 3 EMI C4 22 -0.11 12.011 ;
qtot 0.78
48 opls_557 3 EMI N5 23 0.15 14.0067 ;
qtot 0.93
49 opls_135 3 EMI C6 24 -0.17 12.011 ;
qtot 0.76
50 opls_136 3 EMI C7 25 -0.05 12.011 ;
qtot 0.71
51 opls_135 3 EMI C8 26 -0.17 12.011 ;
qtot 0.54
52 opls_564 3 EMI H9 27 0.21 1.008 ;
qtot 0.75
53 opls_564 3 EMI H10 27 0.21 1.008 ;
qtot 0.96
54 opls_563 3 EMI H11 27 0.21 1.008 ;
qtot 1.17
55 opls_140 3 EMI H12 28 0.13 1.008 ;
qtot 1.3
56 opls_140 3 EMI H13 28 0.13 1.008 ;
qtot 1.43
57 opls_140 3 EMI H14 28 0.13 1.008 ;
qtot 1.56
58 opls_140 3 EMI H15 29 0.13 1.008 ;
qtot 1.69
59 opls_140 3 EMI H16 29 0.13 1.008 ;
qtot 1.82
60 opls_140 3 EMI H17 30 0.06 1.008 ;
qtot 1.88
61 opls_140 3 EMI H18 30 0.06 1.008 ;
qtot 1.94
62 opls_140 3 EMI H19 30 0.06 1.008 ;
qtot 2
63 opls_561 4 EMI C 31 -0.13 12.011 ;
qtot 1.87
64 opls_561 4 EMI C2 32 -0.13 12.011 ;
qtot 1.74
65 opls_557 4 EMI N3 33 0.15 14.0067 ;
qtot 1.89
66 opls_558 4 EMI C4 34 -0.11 12.011 ;
qtot 1.78
67 opls_557 4 EMI N5 35 0.15 14.0067 ;
qtot 1.93
68 opls_135 4 EMI C6 36 -0.17 12.011 ;
qtot 1.76
69 opls_136 4 EMI C7 37 -0.05 12.011 ;
qtot 1.71
70 opls_135 4 EMI C8 38 -0.17 12.011 ;
qtot 1.54
71 opls_564 4 EMI H9 39 0.21 1.008 ;
qtot 1.75
72 opls_564 4 EMI H10 39 0.21 1.008 ;
qtot 1.96
73 opls_563 4 EMI H11 39 0.21 1.008 ;
qtot 2.17
74 opls_140 4 EMI H12 40 0.13 1.008 ;
qtot 2.3
75 opls_140 4 EMI H13 40 0.13 1.008 ;
qtot 2.43
76 opls_140 4 EMI H14 40 0.13 1.008 ;
qtot 2.56
77 opls_140 4 EMI H15 41 0.13 1.008 ;
qtot 2.69
78 opls_140 4 EMI H16 41 0.13 1.008 ;
qtot 2.82
79 opls_140 4 EMI H17 42 0.06 1.008 ;
qtot 2.88
80 opls_140 4 EMI H18 42 0.06 1.008 ;
qtot 2.94
81 opls_140 4 EMI H19 42 0.06 1.008 ;
qtot 3
82 opls_561 5 EMI C 43 -0.13 12.011 ;
qtot 2.87
83 opls_561 5 EMI C2 44 -0.13 12.011 ;
qtot 2.74
84 opls_557 5 EMI N3 45 0.15 14.0067 ;
qtot 2.89
85 opls_558 5 EMI C4 46 -0.11 12.011 ;
qtot 2.78
86 opls_557 5 EMI N5 47 0.15 14.0067 ;
qtot 2.93
87 opls_135 5 EMI C6 48 -0.17 12.011 ;
qtot 2.76
88 opls_136 5 EMI C7 49 -0.05 12.011 ;
qtot 2.71
89 opls_135 5 EMI C8 50 -0.17 12.011 ;
qtot 2.54
90 opls_564 5 EMI H9 51 0.21 1.008 ;
qtot 2.75
91 opls_564 5 EMI H10 51 0.21 1.008 ;
qtot 2.96
92 opls_563 5 EMI H11 51 0.21 1.008 ;
qtot 3.17
93 opls_140 5 EMI H12 52 0.13 1.008 ;
qtot 3.3
94 opls_140 5 EMI H13 52 0.13 1.008 ;
qtot 3.43
95 opls_140 5 EMI H14 52 0.13 1.008 ;
qtot 3.56
96 opls_140 5 EMI H15 53 0.13 1.008 ;
qtot 3.69
97 opls_140 5 EMI H16 53 0.13 1.008 ;
qtot 3.82
98 opls_140 5 EMI H17 54 0.06 1.008 ;
qtot 3.88
99 opls_140 5 EMI H18 54 0.06 1.008 ;
qtot 3.94
100 opls_140 5 EMI H19 54 0.06 1.008 ;
qtot 4
101 opls_561 6 EMI C 55 -0.13 12.011 ;
qtot 3.87
102 opls_561 6 EMI C2 56 -0.13 12.011 ;
qtot 3.74
103 opls_557 6 EMI N3 57 0.15 14.0067 ;
qtot 3.89
104 opls_558 6 EMI C4 58 -0.11 12.011 ;
qtot 3.78
105 opls_557 6 EMI N5 59 0.15 14.0067 ;
qtot 3.93
106 opls_135 6 EMI C6 60 -0.17 12.011 ;
qtot 3.76
107 opls_136 6 EMI C7 61 -0.05 12.011 ;
qtot 3.71
108 opls_135 6 EMI C8 62 -0.17 12.011 ;
qtot 3.54
109 opls_564 6 EMI H9 63 0.21 1.008 ;
qtot 3.75
110 opls_564 6 EMI H10 63 0.21 1.008 ;
qtot 3.96
111 opls_563 6 EMI H11 63 0.21 1.008 ;
qtot 4.17
112 opls_140 6 EMI H12 64 0.13 1.008 ;
qtot 4.3
113 opls_140 6 EMI H13 64 0.13 1.008 ;
qtot 4.43
114 opls_140 6 EMI H14 64 0.13 1.008 ;
qtot 4.56
115 opls_140 6 EMI H15 65 0.13 1.008 ;
qtot 4.69
116 opls_140 6 EMI H16 65 0.13 1.008 ;
qtot 4.82
117 opls_140 6 EMI H17 66 0.06 1.008 ;
qtot 4.88
118 opls_140 6 EMI H18 66 0.06 1.008 ;
qtot 4.94
119 opls_140 6 EMI H19 66 0.06 1.008 ;
qtot 5
120 opls_561 7 EMI C 67 -0.13 12.011 ;
qtot 4.87
121 opls_561 7 EMI C2 68 -0.13 12.011 ;
qtot 4.74
122 opls_557 7 EMI N3 69 0.15 14.0067 ;
qtot 4.89
123 opls_558 7 EMI C4 70 -0.11 12.011 ;
qtot 4.78
124 opls_557 7 EMI N5 71 0.15 14.0067 ;
qtot 4.93
125 opls_135 7 EMI C6 72 -0.17 12.011 ;
qtot 4.76
126 opls_136 7 EMI C7 73 -0.05 12.011 ;
qtot 4.71
127 opls_135 7 EMI C8 74 -0.17 12.011 ;
qtot 4.54
128 opls_564 7 EMI H9 75 0.21 1.008 ;
qtot 4.75
129 opls_564 7 EMI H10 75 0.21 1.008 ;
qtot 4.96
130 opls_563 7 EMI H11 75 0.21 1.008 ;
qtot 5.17
131 opls_140 7 EMI H12 76 0.13 1.008 ;
qtot 5.3
132 opls_140 7 EMI H13 76 0.13 1.008 ;
qtot 5.43
133 opls_140 7 EMI H14 76 0.13 1.008 ;
qtot 5.56
134 opls_140 7 EMI H15 77 0.13 1.008 ;
qtot 5.69
135 opls_140 7 EMI H16 77 0.13 1.008 ;
qtot 5.82
136 opls_140 7 EMI H17 78 0.06 1.008 ;
qtot 5.88
137 opls_140 7 EMI H18 78 0.06 1.008 ;
qtot 5.94
138 opls_140 7 EMI H19 78 0.06 1.008 ;
qtot 6
139 opls_561 8 EMI C 79 -0.13 12.011 ;
qtot 5.87
140 opls_561 8 EMI C2 80 -0.13 12.011 ;
qtot 5.74
141 opls_557 8 EMI N3 81 0.15 14.0067 ;
qtot 5.89
142 opls_558 8 EMI C4 82 -0.11 12.011 ;
qtot 5.78
143 opls_557 8 EMI N5 83 0.15 14.0067 ;
qtot 5.93
144 opls_135 8 EMI C6 84 -0.17 12.011 ;
qtot 5.76
145 opls_136 8 EMI C7 85 -0.05 12.011 ;
qtot 5.71
146 opls_135 8 EMI C8 86 -0.17 12.011 ;
qtot 5.54
147 opls_564 8 EMI H9 87 0.21 1.008 ;
qtot 5.75
148 opls_564 8 EMI H10 87 0.21 1.008 ;
qtot 5.96
149 opls_563 8 EMI H11 87 0.21 1.008 ;
qtot 6.17
150 opls_140 8 EMI H12 88 0.13 1.008 ;
qtot 6.3
151 opls_140 8 EMI H13 88 0.13 1.008 ;
qtot 6.43
152 opls_140 8 EMI H14 88 0.13 1.008 ;
qtot 6.56
153 opls_140 8 EMI H15 89 0.13 1.008 ;
qtot 6.69
154 opls_140 8 EMI H16 89 0.13 1.008 ;
qtot 6.82
155 opls_140 8 EMI H17 90 0.06 1.008 ;
qtot 6.88
156 opls_140 8 EMI H18 90 0.06 1.008 ;
qtot 6.94
157 opls_140 8 EMI H19 90 0.06 1.008 ;
qtot 7
158 opls_561 9 EMI C 91 -0.13 12.011 ;
qtot 6.87
159 opls_561 9 EMI C2 92 -0.13 12.011 ;
qtot 6.74
160 opls_557 9 EMI N3 93 0.15 14.0067 ;
qtot 6.89
161 opls_558 9 EMI C4 94 -0.11 12.011 ;
qtot 6.78
162 opls_557 9 EMI N5 95 0.15 14.0067 ;
qtot 6.93
163 opls_135 9 EMI C6 96 -0.17 12.011 ;
qtot 6.76
164 opls_136 9 EMI C7 97 -0.05 12.011 ;
qtot 6.71
165 opls_135 9 EMI C8 98 -0.17 12.011 ;
qtot 6.54
166 opls_564 9 EMI H9 99 0.21 1.008 ;
qtot 6.75
167 opls_564 9 EMI H10 99 0.21 1.008 ;
qtot 6.96
168 opls_563 9 EMI H11 99 0.21 1.008 ;
qtot 7.17
169 opls_140 9 EMI H12 100 0.13 1.008 ;
qtot 7.3
170 opls_140 9 EMI H13 100 0.13 1.008 ;
qtot 7.43
171 opls_140 9 EMI H14 100 0.13 1.008 ;
qtot 7.56
172 opls_140 9 EMI H15 101 0.13 1.008 ;
qtot 7.69
173 opls_140 9 EMI H16 101 0.13 1.008 ;
qtot 7.82
174 opls_140 9 EMI H17 102 0.06 1.008 ;
qtot 7.88
175 opls_140 9 EMI H18 102 0.06 1.008 ;
qtot 7.94
176 opls_140 9 EMI H19 102 0.06 1.008 ;
qtot 8
177 opls_561 10 EMI C 103 -0.13 12.011 ;
qtot 7.87
178 opls_561 10 EMI C2 104 -0.13 12.011 ;
qtot 7.74
179 opls_557 10 EMI N3 105 0.15 14.0067 ;
qtot 7.89
180 opls_558 10 EMI C4 106 -0.11 12.011 ;
qtot 7.78
181 opls_557 10 EMI N5 107 0.15 14.0067 ;
qtot 7.93
182 opls_135 10 EMI C6 108 -0.17 12.011 ;
qtot 7.76
183 opls_136 10 EMI C7 109 -0.05 12.011 ;
qtot 7.71
184 opls_135 10 EMI C8 110 -0.17 12.011 ;
qtot 7.54
185 opls_564 10 EMI H9 111 0.21 1.008 ;
qtot 7.75
186 opls_564 10 EMI H10 111 0.21 1.008 ;
qtot 7.96
187 opls_563 10 EMI H11 111 0.21 1.008 ;
qtot 8.17
188 opls_140 10 EMI H12 112 0.13 1.008 ;
qtot 8.3
189 opls_140 10 EMI H13 112 0.13 1.008 ;
qtot 8.43
190 opls_140 10 EMI H14 112 0.13 1.008 ;
qtot 8.56
191 opls_140 10 EMI H15 113 0.13 1.008 ;
qtot 8.69
192 opls_140 10 EMI H16 113 0.13 1.008 ;
qtot 8.82
193 opls_140 10 EMI H17 114 0.06 1.008 ;
qtot 8.88
194 opls_140 10 EMI H18 114 0.06 1.008 ;
qtot 8.94
195 opls_140 10 EMI H19 114 0.06 1.008 ;
qtot 9
196 opls_561 11 EMI C 115 -0.13 12.011 ;
qtot 8.87
197 opls_561 11 EMI C2 116 -0.13 12.011 ;
qtot 8.74
198 opls_557 11 EMI N3 117 0.15 14.0067 ;
qtot 8.89
199 opls_558 11 EMI C4 118 -0.11 12.011 ;
qtot 8.78
200 opls_557 11 EMI N5 119 0.15 14.0067 ;
qtot 8.93
201 opls_135 11 EMI C6 120 -0.17 12.011 ;
qtot 8.76
202 opls_136 11 EMI C7 121 -0.05 12.011 ;
qtot 8.71
203 opls_135 11 EMI C8 122 -0.17 12.011 ;
qtot 8.54
204 opls_564 11 EMI H9 123 0.21 1.008 ;
qtot 8.75
205 opls_564 11 EMI H10 123 0.21 1.008 ;
qtot 8.96
206 opls_563 11 EMI H11 123 0.21 1.008 ;
qtot 9.17
207 opls_140 11 EMI H12 124 0.13 1.008 ;
qtot 9.3
208 opls_140 11 EMI H13 124 0.13 1.008 ;
qtot 9.43
209 opls_140 11 EMI H14 124 0.13 1.008 ;
qtot 9.56
210 opls_140 11 EMI H15 125 0.13 1.008 ;
qtot 9.69
211 opls_140 11 EMI H16 125 0.13 1.008 ;
qtot 9.82
212 opls_140 11 EMI H17 126 0.06 1.008 ;
qtot 9.88
213 opls_140 11 EMI H18 126 0.06 1.008 ;
qtot 9.94
214 opls_140 11 EMI H19 126 0.06 1.008 ;
qtot 10
215 opls_561 12 EMI C 127 -0.13 12.011 ;
qtot 9.87
216 opls_561 12 EMI C2 128 -0.13 12.011 ;
qtot 9.74
217 opls_557 12 EMI N3 129 0.15 14.0067 ;
qtot 9.89
218 opls_558 12 EMI C4 130 -0.11 12.011 ;
qtot 9.78
219 opls_557 12 EMI N5 131 0.15 14.0067 ;
qtot 9.93
220 opls_135 12 EMI C6 132 -0.17 12.011 ;
qtot 9.76
221 opls_136 12 EMI C7 133 -0.05 12.011 ;
qtot 9.71
222 opls_135 12 EMI C8 134 -0.17 12.011 ;
qtot 9.54
223 opls_564 12 EMI H9 135 0.21 1.008 ;
qtot 9.75
224 opls_564 12 EMI H10 135 0.21 1.008 ;
qtot 9.96
225 opls_563 12 EMI H11 135 0.21 1.008 ;
qtot 10.17
226 opls_140 12 EMI H12 136 0.13 1.008 ;
qtot 10.3
227 opls_140 12 EMI H13 136 0.13 1.008 ;
qtot 10.43
228 opls_140 12 EMI H14 136 0.13 1.008 ;
qtot 10.56
229 opls_140 12 EMI H15 137 0.13 1.008 ;
qtot 10.69
230 opls_140 12 EMI H16 137 0.13 1.008 ;
qtot 10.82
231 opls_140 12 EMI H17 138 0.06 1.008 ;
qtot 10.88
232 opls_140 12 EMI H18 138 0.06 1.008 ;
qtot 10.94
233 opls_140 12 EMI H19 138 0.06 1.008 ;
qtot 11
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