[gmx-users] simulation with position constraint by a harmonic potential
Liu, Liang
liu4gre at gmail.com
Tue Sep 27 00:13:10 CEST 2011
Thanks for the information.
It looks the pdb2gmx can generate the posre.itp file and what I use is "pdb2gmx
-ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce".
The file shows:
; 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
3 1 1000 1000 1000
6 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
11 1 1000 1000 1000
12 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
20 1 1000 1000 1000
21 1 1000 1000 1000
23 1 1000 1000 1000
24 1 1000 1000 1000
25 1 1000 1000 1000
27 1 1000 1000 1000
29 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
36 1 1000 1000 1000
39 1 1000 1000 1000
41 1 1000 1000 1000
42 1 1000 1000 1000
44 1 1000 1000 1000
45 1 1000 1000 1000
47 1 1000 1000 1000
49 1 1000 1000 1000
50 1 1000 1000 1000
51 1 1000 1000 1000
53 1 1000 1000 1000
54 1 1000 1000 1000
55 1 1000 1000 1000
57 1 1000 1000 1000
59 1 1000 1000 1000
61 1 1000 1000 1000
62 1 1000 1000 1000
63 1 1000 1000 1000
64 1 1000 1000 1000
65 1 1000 1000 1000
66 1 1000 1000 1000
69 1 1000 1000 1000
71 1 1000 1000 1000
72 1 1000 1000 1000
74 1 1000 1000 1000
75 1 1000 1000 1000
77 1 1000 1000 1000
78 1 1000 1000 1000
79 1 1000 1000 1000
80 1 1000 1000 1000
81 1 1000 1000 1000
83 1 1000 1000 1000
84 1 1000 1000 1000
87 1 1000 1000 1000
88 1 1000 1000 1000
89 1 1000 1000 1000
91 1 1000 1000 1000
93 1 1000 1000 1000
95 1 1000 1000 1000
96 1 1000 1000 1000
97 1 1000 1000 1000
98 1 1000 1000 1000
99 1 1000 1000 1000
100 1 1000 1000 1000
103 1 1000 1000 1000
105 1 1000 1000 1000
106 1 1000 1000 1000
108 1 1000 1000 1000
109 1 1000 1000 1000
111 1 1000 1000 1000
113 1 1000 1000 1000
114 1 1000 1000 1000
117 1 1000 1000 1000
118 1 1000 1000 1000
119 1 1000 1000 1000
120 1 1000 1000 1000
122 1 1000 1000 1000
124 1 1000 1000 1000
126 1 1000 1000 1000
127 1 1000 1000 1000
128 1 1000 1000 1000
129 1 1000 1000 1000
130 1 1000 1000 1000
131 1 1000 1000 1000
134 1 1000 1000 1000
136 1 1000 1000 1000
137 1 1000 1000 1000
139 1 1000 1000 1000
140 1 1000 1000 1000
142 1 1000 1000 1000
144 1 1000 1000 1000
145 1 1000 1000 1000
146 1 1000 1000 1000
148 1 1000 1000 1000
149 1 1000 1000 1000
150 1 1000 1000 1000
152 1 1000 1000 1000
154 1 1000 1000 1000
156 1 1000 1000 1000
157 1 1000 1000 1000
158 1 1000 1000 1000
159 1 1000 1000 1000
160 1 1000 1000 1000
161 1 1000 1000 1000
164 1 1000 1000 1000
166 1 1000 1000 1000
167 1 1000 1000 1000
169 1 1000 1000 1000
170 1 1000 1000 1000
172 1 1000 1000 1000
174 1 1000 1000 1000
175 1 1000 1000 1000
176 1 1000 1000 1000
178 1 1000 1000 1000
179 1 1000 1000 1000
180 1 1000 1000 1000
182 1 1000 1000 1000
184 1 1000 1000 1000
186 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
194 1 1000 1000 1000
196 1 1000 1000 1000
197 1 1000 1000 1000
199 1 1000 1000 1000
200 1 1000 1000 1000
202 1 1000 1000 1000
203 1 1000 1000 1000
204 1 1000 1000 1000
205 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
215 1 1000 1000 1000
217 1 1000 1000 1000
219 1 1000 1000 1000
220 1 1000 1000 1000
221 1 1000 1000 1000
222 1 1000 1000 1000
223 1 1000 1000 1000
224 1 1000 1000 1000
227 1 1000 1000 1000
229 1 1000 1000 1000
230 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
241 1 1000 1000 1000
242 1 1000 1000 1000
244 1 1000 1000 1000
245 1 1000 1000 1000
246 1 1000 1000 1000
248 1 1000 1000 1000
250 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
260 1 1000 1000 1000
262 1 1000 1000 1000
263 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
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
281 1 1000 1000 1000
283 1 1000 1000 1000
285 1 1000 1000 1000
286 1 1000 1000 1000
287 1 1000 1000 1000
288 1 1000 1000 1000
289 1 1000 1000 1000
290 1 1000 1000 1000
293 1 1000 1000 1000
295 1 1000 1000 1000
296 1 1000 1000 1000
298 1 1000 1000 1000
299 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
307 1 1000 1000 1000
308 1 1000 1000 1000
311 1 1000 1000 1000
312 1 1000 1000 1000
313 1 1000 1000 1000
315 1 1000 1000 1000
317 1 1000 1000 1000
319 1 1000 1000 1000
320 1 1000 1000 1000
321 1 1000 1000 1000
322 1 1000 1000 1000
323 1 1000 1000 1000
324 1 1000 1000 1000
327 1 1000 1000 1000
329 1 1000 1000 1000
330 1 1000 1000 1000
332 1 1000 1000 1000
333 1 1000 1000 1000
335 1 1000 1000 1000
337 1 1000 1000 1000
338 1 1000 1000 1000
341 1 1000 1000 1000
342 1 1000 1000 1000
343 1 1000 1000 1000
344 1 1000 1000 1000
346 1 1000 1000 1000
348 1 1000 1000 1000
350 1 1000 1000 1000
351 1 1000 1000 1000
352 1 1000 1000 1000
353 1 1000 1000 1000
354 1 1000 1000 1000
355 1 1000 1000 1000
358 1 1000 1000 1000
360 1 1000 1000 1000
361 1 1000 1000 1000
363 1 1000 1000 1000
364 1 1000 1000 1000
366 1 1000 1000 1000
367 1 1000 1000 1000
368 1 1000 1000 1000
369 1 1000 1000 1000
372 1 1000 1000 1000
373 1 1000 1000 1000
375 1 1000 1000 1000
376 1 1000 1000 1000
377 1 1000 1000 1000
379 1 1000 1000 1000
381 1 1000 1000 1000
383 1 1000 1000 1000
384 1 1000 1000 1000
385 1 1000 1000 1000
386 1 1000 1000 1000
387 1 1000 1000 1000
388 1 1000 1000 1000
391 1 1000 1000 1000
393 1 1000 1000 1000
394 1 1000 1000 1000
396 1 1000 1000 1000
397 1 1000 1000 1000
399 1 1000 1000 1000
401 1 1000 1000 1000
402 1 1000 1000 1000
403 1 1000 1000 1000
405 1 1000 1000 1000
406 1 1000 1000 1000
407 1 1000 1000 1000
409 1 1000 1000 1000
411 1 1000 1000 1000
413 1 1000 1000 1000
So how to adjust the force constraint to the harmonic poteitial E =
k(r-r0)^2, with different values of k?
I am totally a new user of Gromacs, even MD simulation. Please help, Thanks
a lot.
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Liu, Liang wrote:
>
>> Firstly I want to thank for your reply, yes, it should be position
>> restraint.
>>
>> I don't know how to reply in the thread, actually that was my first post.
>> Therefore I have to ask you here, hope it also work to you.
>>
>>
> Simply reply to the message. The discussion needs to stay on the list.
> The members are not private tutors.
>
> My question is how to perform a position restraint simulation with the
>> heavy atom constrained to its initial position by a harmonic potential
>> E=k(r-r0)^2,
>> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?
>>
>>
> You can adjust the force constant in the posre.itp file. There is no
> automated way of decreasing or increasing a restraint; independent
> simulations must be run on the different topologies.
>
> -Justin
>
> Thanks, and any helps will be highly appreciated.
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
--
Best,
Liang Liu
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