Gromacs

.itp **
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
12 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
19 1 1000 1000 1000
21 1 1000 1000 1000
22 1 1000 1000 1000
23 1 1000 1000 1000
24 1 1000 1000 1000
25 1 1000 1000 1000
27 1 1000 1000 1000
28 1 1000 1000 1000
29 1 1000 1000 1000
30 1 1000 1000 1000
31 1 1000 1000 1000
32 1 1000 1000 1000
33 1 1000 1000 1000
34 1 1000 1000 1000
35 1 1000 1000 1000
37 1 1000 1000 1000
38 1 1000 1000 1000
39 1 1000 1000 1000
40 1 1000 1000 1000
41 1 1000 1000 1000
42 1 1000 1000 1000
43 1 1000 1000 1000
44 1 1000 1000 1000
46 1 1000 1000 1000
47 1 1000 1000 1000
48 1 1000 1000 1000
49 1 1000 1000 1000
51 1 1000 1000 1000
53 1 1000 1000 1000
55 1 1000 1000 1000
57 1 1000 1000 1000
58 1 1000 1000 1000
60 1 1000 1000 1000
61 1 1000 1000 1000
62 1 1000 1000 1000
64 1 1000 1000 1000
65 1 1000 1000 1000
66 1 1000 1000 1000
67 1 1000 1000 1000
69 1 1000 1000 1000
70 1 1000 1000 1000
71 1 1000 1000 1000
72 1 1000 1000 1000
73 1 1000 1000 1000
74 1 1000 1000 1000
78 1 1000 1000 1000
79 1 1000 1000 1000
80 1 1000 1000 1000
82 1 1000 1000 1000
83 1 1000 1000 1000
84 1 1000 1000 1000
85 1 1000 1000 1000
86 1 1000 1000 1000
87 1 1000 1000 1000
89 1 1000 1000 1000
90 1 1000 1000 1000
91 1 1000 1000 1000
93 1 1000 1000 1000
94 1 1000 1000 1000
95 1 1000 1000 1000
96 1 1000 1000 1000
98 1 1000 1000 1000
99 1 1000 1000 1000
100 1 1000 1000 1000
101 1 1000 1000 1000
103 1 1000 1000 1000
104 1 1000 1000 1000
106 1 1000 1000 1000
107 1 1000 1000 1000
109 1 1000 1000 1000
111 1 1000 1000 1000
113 1 1000 1000 1000
115 1 1000 1000 1000
116 1 1000 1000 1000
117 1 1000 1000 1000
119 1 1000 1000 1000
120 1 1000 1000 1000
121 1 1000 1000 1000
122 1 1000 1000 1000
124 1 1000 1000 1000
125 1 1000 1000 1000
126 1 1000 1000 1000
127 1 1000 1000 1000
129 1 1000 1000 1000
130 1 1000 1000 1000
131 1 1000 1000 1000
133 1 1000 1000 1000
134 1 1000 1000 1000
135 1 1000 1000 1000
136 1 1000 1000 1000
138 1 1000 1000 1000
139 1 1000 1000 1000
140 1 1000 1000 1000
141 1 1000 1000 1000
142 1 1000 1000 1000
143 1 1000 1000 1000
147 1 1000 1000 1000
148 1 1000 1000 1000
149 1 1000 1000 1000
151 1 1000 1000 1000
152 1 1000 1000 1000
153 1 1000 1000 1000
154 1 1000 1000 1000
155 1 1000 1000 1000
156 1 1000 1000 1000
158 1 1000 1000 1000
159 1 1000 1000 1000
160 1 1000 1000 1000
161 1 1000 1000 1000
162 1 1000 1000 1000
163 1 1000 1000 1000
165 1 1000 1000 1000
166 1 1000 1000 1000
167 1 1000 1000 1000
168 1 1000 1000 1000
169 1 1000 1000 1000
171 1 1000 1000 1000
172 1 1000 1000 1000
175 1 1000 1000 1000
178 1 1000 1000 1000
179 1 1000 1000 1000
180 1 1000 1000 1000
182 1 1000 1000 1000
183 1 1000 1000 1000
184 1 1000 1000 1000
185 1 1000 1000 1000
187 1 1000 1000 1000
188 1 1000 1000 1000
189 1 1000 1000 1000
190 1 1000 1000 1000
191 1 1000 1000 1000
193 1 1000 1000 1000
194 1 1000 1000 1000
197 1 1000 1000 1000
200 1 1000 1000 1000
201 1 1000 1000 1000
202 1 1000 1000 1000
203 1 1000 1000 1000
204 1 1000 1000 1000
205 1 1000 1000 1000
206 1 1000 1000 1000
207 1 1000 1000 1000
208 1 1000 1000 1000
209 1 1000 1000 1000
211 1 1000 1000 1000
212 1 1000 1000 1000
213 1 1000 1000 1000
214 1 1000 1000 1000
215 1 1000 1000 1000
216 1 1000 1000 1000
218 1 1000 1000 1000
219 1 1000 1000 1000
220 1 1000 1000 1000
221 1 1000 1000 1000
222 1 1000 1000 1000
224 1 1000 1000 1000
225 1 1000 1000 1000
228 1 1000 1000 1000
231 1 1000 1000 1000
232 1 1000 1000 1000
233 1 1000 1000 1000
235 1 1000 1000 1000
236 1 1000 1000 1000
237 1 1000 1000 1000
238 1 1000 1000 1000
239 1 1000 1000 1000
240 1 1000 1000 1000
242 1 1000 1000 1000
243 1 1000 1000 1000
244 1 1000 1000 1000
246 1 1000 1000 1000
247 1 1000 1000 1000
248 1 1000 1000 1000
250 1 1000 1000 1000
251 1 1000 1000 1000
252 1 1000 1000 1000
253 1 1000 1000 1000
254 1 1000 1000 1000
255 1 1000 1000 1000
256 1 1000 1000 1000
257 1 1000 1000 1000
259 1 1000 1000 1000
260 1 1000 1000 1000
261 1 1000 1000 1000
262 1 1000 1000 1000
263 1 1000 1000 1000
264 1 1000 1000 1000
265 1 1000 1000 1000
266 1 1000 1000 1000
268 1 1000 1000 1000
269 1 1000 1000 1000
270 1 1000 1000 1000
271 1 1000 1000 1000
273 1 1000 1000 1000
274 1 1000 1000 1000
275 1 1000 1000 1000
277 1 1000 1000 1000
278 1 1000 1000 1000
279 1 1000 1000 1000
280 1 1000 1000 1000
282 1 1000 1000 1000
283 1 1000 1000 1000
284 1 1000 1000 1000
285 1 1000 1000 1000
286 1 1000 1000 1000
289 1 1000 1000 1000
290 1 1000 1000 1000
291 1 1000 1000 1000
293 1 1000 1000 1000
294 1 1000 1000 1000
295 1 1000 1000 1000
296 1 1000 1000 1000
297 1 1000 1000 1000
298 1 1000 1000 1000
300 1 1000 1000 1000
301 1 1000 1000 1000
302 1 1000 1000 1000
303 1 1000 1000 1000
304 1 1000 1000 1000
305 1 1000 1000 1000
306 1 1000 1000 1000
307 1 1000 1000 1000
308 1 1000 1000 1000
310 1 1000 1000 1000
311 1 1000 1000 1000
312 1 1000 1000 1000
313 1 1000 1000 1000; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
12 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
19 1 1000 1000 1000
21 1 1000 1000 1000
22 1 1000 1000 1000
23 1 1000 1000 1000
24 1 1000 1000 1000
25 1 1000 1000 1000
27 1 1000 1000 1000
28 1 1000 1000 1000
29 1 1000 1000 1000
30 1 1000 1000 1000
31 1 1000 1000 1000
32 1 1000 1000 1000
33 1 1000 1000 1000
34 1 1000 1000 1000
35 1 1000 1000 1000
37 1 1000 1000 1000
38 1 1000 1000 1000
39 1 1000 1000 1000
40 1 1000 1000 1000
41 1 1000 1000 1000
42 1 1000 1000 1000
43 1 1000 1000 1000
44 1 1000 1000 1000
46 1 1000 1000 1000
47 1 1000 1000 1000
48 1 1000 1000 1000
49 1 1000 1000 1000
51 1 1000 1000 1000
53 1 1000 1000 1000
55 1 1000 1000 1000
57 1 1000 1000 1000
58 1 1000 1000 1000
60 1 1000 1000 1000
61 1 1000 1000 1000
62 1 1000 1000 1000
64 1 1000 1000 1000
65 1 1000 1000 1000
66 1 1000 1000 1000
67 1 1000 1000 1000
69 1 1000 1000 1000
70 1 1000 1000 1000
71 1 1000 1000 1000
72 1 1000 1000 1000
73 1 1000 1000 1000
74 1 1000 1000 1000
78 1 1000 1000 1000
79 1 1000 1000 1000
80 1 1000 1000 1000
82 1 1000 1000 1000
83 1 1000 1000 1000
84 1 1000 1000 1000
85 1 1000 1000 1000
86 1 1000 1000 1000
87 1 1000 1000 1000
89 1 1000 1000 1000
90 1 1000 1000 1000
91 1 1000 1000 1000
93 1 1000 1000 1000
94 1 1000 1000 1000
95 1 1000 1000 1000
96 1 1000 1000 1000
98 1 1000 1000 1000
99 1 1000 1000 1000
100 1 1000 1000 1000
101 1 1000 1000 1000
103 1 1000 1000 1000
104 1 1000 1000 1000
106 1 1000 1000 1000
107 1 1000 1000 1000
109 1 1000 1000 1000
111 1 1000 1000 1000
113 1 1000 1000 1000
115 1 1000 1000 1000
116 1 1000 1000 1000
117 1 1000 1000 1000
119 1 1000 1000 1000
120 1 1000 1000 1000
121 1 1000 1000 1000
122 1 1000 1000 1000
124 1 1000 1000 1000
125 1 1000 1000 1000
126 1 1000 1000 1000
127 1 1000 1000 1000
129 1 1000 1000 1000
130 1 1000 1000 1000
131 1 1000 1000 1000
133 1 1000 1000 1000
134 1 1000 1000 1000
135 1 1000 1000 1000
136 1 1000 1000 1000
138 1 1000 1000 1000
139 1 1000 1000 1000
140 1 1000 1000 1000
141 1 1000 1000 1000
142 1 1000 1000 1000
143 1 1000 1000 1000
147 1 1000 1000 1000
148 1 1000 1000 1000
149 1 1000 1000 1000
151 1 1000 1000 1000
152 1 1000 1000 1000
153 1 1000 1000 1000
154 1 1000 1000 1000
155 1 1000 1000 1000
156 1 1000 1000 1000
158 1 1000 1000 1000
159 1 1000 1000 1000
160 1 1000 1000 1000
161 1 1000 1000 1000
162 1 1000 1000 1000
163 1 1000 1000 1000
165 1 1000 1000 1000
166 1 1000 1000 1000
167 1 1000 1000 1000
168 1 1000 1000 1000
169 1 1000 1000 1000
171 1 1000 1000 1000
172 1 1000 1000 1000
175 1 1000 1000 1000
178 1 1000 1000 1000
179 1 1000 1000 1000
180 1 1000 1000 1000
182 1 1000 1000 1000
183 1 1000 1000 1000
184 1 1000 1000 1000
185 1 1000 1000 1000
187 1 1000 1000 1000
188 1 1000 1000 1000
189 1 1000 1000 1000
190 1 1000 1000 1000
191 1 1000 1000 1000
193 1 1000 1000 1000
194 1 1000 1000 1000
197 1 1000 1000 1000
200 1 1000 1000 1000
201 1 1000 1000 1000
202 1 1000 1000 1000
203 1 1000 1000 1000
204 1 1000 1000 1000
205 1 1000 1000 1000
206 1 1000 1000 1000
207 1 1000 1000 1000
208 1 1000 1000 1000
209 1 1000 1000 1000
211 1 1000 1000 1000
212 1 1000 1000 1000
213 1 1000 1000 1000
214 1 1000 1000 1000
215 1 1000 1000 1000
216 1 1000 1000 1000
218 1 1000 1000 1000
219 1 1000 1000 1000
220 1 1000 1000 1000
221 1 1000 1000 1000
222 1 1000 1000 1000
224 1 1000 1000 1000
225 1 1000 1000 1000
228 1 1000 1000 1000
231 1 1000 1000 1000
232 1 1000 1000 1000
233 1 1000 1000 1000
235 1 1000 1000 1000
236 1 1000 1000 1000
237 1 1000 1000 1000
238 1 1000 1000 1000
239 1 1000 1000 1000
240 1 1000 1000 1000
242 1 1000 1000 1000
243 1 1000 1000 1000
244 1 1000 1000 1000
246 1 1000 1000 1000
247 1 1000 1000 1000
248 1 1000 1000 1000
250 1 1000 1000 1000
251 1 1000 1000 1000
252 1 1000 1000 1000
253 1 1000 1000 1000
254 1 1000 1000 1000
255 1 1000 1000 1000
256 1 1000 1000 1000
257 1 1000 1000 1000
259 1 1000 1000 1000
260 1 1000 1000 1000
261 1 1000 1000 1000
262 1 1000 1000 1000
263 1 1000 1000 1000
264 1 1000 1000 1000
265 1 1000 1000 1000
266 1 1000 1000 1000
268 1 1000 1000 1000
269 1 1000 1000 1000
270 1 1000 1000 1000
271 1 1000 1000 1000
273 1 1000 1000 1000
274 1 1000 1000 1000
275 1 1000 1000 1000
277 1 1000 1000 1000
278 1 1000 1000 1000
279 1 1000 1000 1000
280 1 1000 1000 1000
282 1 1000 1000 1000
283 1 1000 1000 1000
284 1 1000 1000 1000
285 1 1000 1000 1000
286 1 1000 1000 1000
289 1 1000 1000 1000
290 1 1000 1000 1000
291 1 1000 1000 1000
293 1 1000 1000 1000
294 1 1000 1000 1000
295 1 1000 1000 1000
296 1 1000 1000 1000
297 1 1000 1000 1000
298 1 1000 1000 1000
300 1 1000 1000 1000
301 1 1000 1000 1000
302 1 1000 1000 1000
303 1 1000 1000 1000
304 1 1000 1000 1000
305 1 1000 1000 1000
306 1 1000 1000 1000
307 1 1000 1000 1000
308 1 1000 1000 1000
310 1 1000 1000 1000
311 1 1000 1000 1000
312 1 1000 1000 1000
313 1 1000 1000 1000
314 1 1000 1000 1000
315 1 1000 1000 1000
317 1 1000 1000 1000
318 1 1000 1000 1000
319 1 1000 1000 1000
321 1 1000 1000 1000
322 1 1000 1000 1000
323 1 1000 1000 1000
324 1 1000 1000 1000
325 1 1000 1000 1000
326 1 1000 1000 1000
327 1 1000 1000 1000
328 1 1000 1000 1000
329 1 1000 1000 1000
330 1 1000 1000 1000
331 1 1000 1000 1000
314 1 1000 1000 1000
315 1 1000 1000 1000
317 1 1000 1000 1000
318 1 1000 1000 1000
319 1 1000 1000 1000
321 1 1000 1000 1000
322 1 1000 1000 1000
323 1 1000 1000 1000
324 1 1000 1000 1000
325 1 1000 1000 1000
326 1 1000 1000 1000
327 1 1000 1000 1000
328 1 1000 1000 1000
329 1 1000 1000 1000
330 1 1000 1000 1000
331 1 1000 1000 1000

.mdp**
title = FWS
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 25000 ; total 50.0 ps.
nstcomm = 1
nstxout = 500 ;
nstvout = 0 ;
nstfout = 0
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = le-5
optimize_fft = yes
; Periodic boudary conditions in all the directions

;Temperature coupling
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
;Pressure coupling
;Pcoupl = berendsen
;tau_p = 0.5
;compressibility = 4.5e-5
;ref_p = 1.0
;Velocity generation at 300K
gen_vel = yes
gen_temp = 300
gen_seed = 173529

pr.log
Log file opened on Thu May 15 00:53:07 2008
Host: localhost.localdomain pid: 5905 nodeid: 0 nnodes: 1
The Gromacs distribution was built Mon Jan 14 02:33:08 IST 2008 by
niamodlacol.tsohlacol|ksd#niamodlacol.tsohlacol|ksd (Linux 2.6.23.1-42.fc8 i686)

:-) G R O M A C S (-:

S C A M O R G

:-) VERSION 3.3.1 (-:

Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) mdrun_mpi (-:

PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-- -- - Thank You - -- --

PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-- -- - Thank You - -- --

Input Parameters:
integrator = md
nsteps = 10000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy = 10
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 35
nky = 28
nkz = 32
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
andersen_seed = 815131
rlist = 0.9
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4 LJ-14 Coulomb-14
4.95969e+02 3.33994e+0

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