<font color="#000099"><font face="verdana,sans-serif">Thanks for the information.</font></font><div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif">It looks the pdb2gmx can generate the posre.itp file and what I use is</font><span class="Apple-style-span" style="color: rgb(0, 0, 153); font-family: verdana, sans-serif; "> "pdb2gmx -ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce".</span></div>
<div><span class="Apple-style-span" style="color: rgb(0, 0, 153); font-family: verdana, sans-serif; ">The file shows:</span></div><div>; In this topology include file, you will find position restraint</div><div>; entries for all the heavy atoms in your original pdb file.</div>
<div>; This means that all the protons which were added by pdb2gmx are</div><div>; not restrained.<span class="Apple-style-span" style="color: rgb(0, 0, 153); font-family: verdana, sans-serif; ">"</span></div><div><span class="Apple-style-span" style="color: rgb(0, 0, 153); font-family: verdana, sans-serif; "><div>
[ position_restraints ]</div><div>; atom type fx fy fz</div><div> 1 1 1000 1000 1000</div><div> 3 1 1000 1000 1000</div><div> 6 1 1000 1000 1000</div><div> 8 1 1000 1000 1000</div>
<div> 9 1 1000 1000 1000</div><div> 11 1 1000 1000 1000</div><div> 12 1 1000 1000 1000</div><div> 14 1 1000 1000 1000</div><div> 15 1 1000 1000 1000</div><div> 16 1 1000 1000 1000</div>
<div> 17 1 1000 1000 1000</div><div> 20 1 1000 1000 1000</div><div> 21 1 1000 1000 1000</div><div> 23 1 1000 1000 1000</div><div> 24 1 1000 1000 1000</div><div> 25 1 1000 1000 1000</div>
<div> 27 1 1000 1000 1000</div><div> 29 1 1000 1000 1000</div><div> 31 1 1000 1000 1000</div><div> 32 1 1000 1000 1000</div><div> 33 1 1000 1000 1000</div><div> 34 1 1000 1000 1000</div>
<div> 35 1 1000 1000 1000</div><div> 36 1 1000 1000 1000</div><div> 39 1 1000 1000 1000</div><div> 41 1 1000 1000 1000</div><div> 42 1 1000 1000 1000</div><div> 44 1 1000 1000 1000</div>
<div> 45 1 1000 1000 1000</div><div> 47 1 1000 1000 1000</div><div> 49 1 1000 1000 1000</div><div> 50 1 1000 1000 1000</div><div> 51 1 1000 1000 1000</div><div> 53 1 1000 1000 1000</div>
<div> 54 1 1000 1000 1000</div><div> 55 1 1000 1000 1000</div><div> 57 1 1000 1000 1000</div><div> 59 1 1000 1000 1000</div><div> 61 1 1000 1000 1000</div><div> 62 1 1000 1000 1000</div>
<div> 63 1 1000 1000 1000</div><div> 64 1 1000 1000 1000</div><div> 65 1 1000 1000 1000</div><div> 66 1 1000 1000 1000</div><div> 69 1 1000 1000 1000</div><div> 71 1 1000 1000 1000</div>
<div> 72 1 1000 1000 1000</div><div> 74 1 1000 1000 1000</div><div> 75 1 1000 1000 1000</div><div> 77 1 1000 1000 1000</div><div> 78 1 1000 1000 1000</div><div> 79 1 1000 1000 1000</div>
<div> 80 1 1000 1000 1000</div><div> 81 1 1000 1000 1000</div><div> 83 1 1000 1000 1000</div><div> 84 1 1000 1000 1000</div><div> 87 1 1000 1000 1000</div><div> 88 1 1000 1000 1000</div>
<div> 89 1 1000 1000 1000</div><div> 91 1 1000 1000 1000</div><div> 93 1 1000 1000 1000</div><div> 95 1 1000 1000 1000</div><div> 96 1 1000 1000 1000</div><div> 97 1 1000 1000 1000</div>
<div> 98 1 1000 1000 1000</div><div> 99 1 1000 1000 1000</div><div> 100 1 1000 1000 1000</div><div> 103 1 1000 1000 1000</div><div> 105 1 1000 1000 1000</div><div> 106 1 1000 1000 1000</div>
<div> 108 1 1000 1000 1000</div><div> 109 1 1000 1000 1000</div><div> 111 1 1000 1000 1000</div><div> 113 1 1000 1000 1000</div><div> 114 1 1000 1000 1000</div><div> 117 1 1000 1000 1000</div>
<div> 118 1 1000 1000 1000</div><div> 119 1 1000 1000 1000</div><div> 120 1 1000 1000 1000</div><div> 122 1 1000 1000 1000</div><div> 124 1 1000 1000 1000</div><div> 126 1 1000 1000 1000</div>
<div> 127 1 1000 1000 1000</div><div> 128 1 1000 1000 1000</div><div> 129 1 1000 1000 1000</div><div> 130 1 1000 1000 1000</div><div> 131 1 1000 1000 1000</div><div> 134 1 1000 1000 1000</div>
<div> 136 1 1000 1000 1000</div><div> 137 1 1000 1000 1000</div><div> 139 1 1000 1000 1000</div><div> 140 1 1000 1000 1000</div><div> 142 1 1000 1000 1000</div><div> 144 1 1000 1000 1000</div>
<div> 145 1 1000 1000 1000</div><div> 146 1 1000 1000 1000</div><div> 148 1 1000 1000 1000</div><div> 149 1 1000 1000 1000</div><div> 150 1 1000 1000 1000</div><div> 152 1 1000 1000 1000</div>
<div> 154 1 1000 1000 1000</div><div> 156 1 1000 1000 1000</div><div> 157 1 1000 1000 1000</div><div> 158 1 1000 1000 1000</div><div> 159 1 1000 1000 1000</div><div> 160 1 1000 1000 1000</div>
<div> 161 1 1000 1000 1000</div><div> 164 1 1000 1000 1000</div><div> 166 1 1000 1000 1000</div><div> 167 1 1000 1000 1000</div><div> 169 1 1000 1000 1000</div><div> 170 1 1000 1000 1000</div>
<div> 172 1 1000 1000 1000</div><div> 174 1 1000 1000 1000</div><div> 175 1 1000 1000 1000</div><div> 176 1 1000 1000 1000</div><div> 178 1 1000 1000 1000</div><div> 179 1 1000 1000 1000</div>
<div> 180 1 1000 1000 1000</div><div> 182 1 1000 1000 1000</div><div> 184 1 1000 1000 1000</div><div> 186 1 1000 1000 1000</div><div> 187 1 1000 1000 1000</div><div> 188 1 1000 1000 1000</div>
<div> 189 1 1000 1000 1000</div><div> 190 1 1000 1000 1000</div><div> 191 1 1000 1000 1000</div><div> 194 1 1000 1000 1000</div><div> 196 1 1000 1000 1000</div><div> 197 1 1000 1000 1000</div>
<div> 199 1 1000 1000 1000</div><div> 200 1 1000 1000 1000</div><div> 202 1 1000 1000 1000</div><div> 203 1 1000 1000 1000</div><div> 204 1 1000 1000 1000</div><div> 205 1 1000 1000 1000</div>
<div> 208 1 1000 1000 1000</div><div> 209 1 1000 1000 1000</div><div> 211 1 1000 1000 1000</div><div> 212 1 1000 1000 1000</div><div> 213 1 1000 1000 1000</div><div> 215 1 1000 1000 1000</div>
<div> 217 1 1000 1000 1000</div><div> 219 1 1000 1000 1000</div><div> 220 1 1000 1000 1000</div><div> 221 1 1000 1000 1000</div><div> 222 1 1000 1000 1000</div><div> 223 1 1000 1000 1000</div>
<div> 224 1 1000 1000 1000</div><div> 227 1 1000 1000 1000</div><div> 229 1 1000 1000 1000</div><div> 230 1 1000 1000 1000</div><div> 232 1 1000 1000 1000</div><div> 233 1 1000 1000 1000</div>
<div> 235 1 1000 1000 1000</div><div> 236 1 1000 1000 1000</div><div> 237 1 1000 1000 1000</div><div> 238 1 1000 1000 1000</div><div> 241 1 1000 1000 1000</div><div> 242 1 1000 1000 1000</div>
<div> 244 1 1000 1000 1000</div><div> 245 1 1000 1000 1000</div><div> 246 1 1000 1000 1000</div><div> 248 1 1000 1000 1000</div><div> 250 1 1000 1000 1000</div><div> 252 1 1000 1000 1000</div>
<div> 253 1 1000 1000 1000</div><div> 254 1 1000 1000 1000</div><div> 255 1 1000 1000 1000</div><div> 256 1 1000 1000 1000</div><div> 257 1 1000 1000 1000</div><div> 260 1 1000 1000 1000</div>
<div> 262 1 1000 1000 1000</div><div> 263 1 1000 1000 1000</div><div> 265 1 1000 1000 1000</div><div> 266 1 1000 1000 1000</div><div> 268 1 1000 1000 1000</div><div> 269 1 1000 1000 1000</div>
<div> 270 1 1000 1000 1000</div><div> 271 1 1000 1000 1000</div><div> 274 1 1000 1000 1000</div><div> 275 1 1000 1000 1000</div><div> 277 1 1000 1000 1000</div><div> 278 1 1000 1000 1000</div>
<div> 279 1 1000 1000 1000</div><div> 281 1 1000 1000 1000</div><div> 283 1 1000 1000 1000</div><div> 285 1 1000 1000 1000</div><div> 286 1 1000 1000 1000</div><div> 287 1 1000 1000 1000</div>
<div> 288 1 1000 1000 1000</div><div> 289 1 1000 1000 1000</div><div> 290 1 1000 1000 1000</div><div> 293 1 1000 1000 1000</div><div> 295 1 1000 1000 1000</div><div> 296 1 1000 1000 1000</div>
<div> 298 1 1000 1000 1000</div><div> 299 1 1000 1000 1000</div><div> 301 1 1000 1000 1000</div><div> 302 1 1000 1000 1000</div><div> 303 1 1000 1000 1000</div><div> 304 1 1000 1000 1000</div>
<div> 305 1 1000 1000 1000</div><div> 307 1 1000 1000 1000</div><div> 308 1 1000 1000 1000</div><div> 311 1 1000 1000 1000</div><div> 312 1 1000 1000 1000</div><div> 313 1 1000 1000 1000</div>
<div> 315 1 1000 1000 1000</div><div> 317 1 1000 1000 1000</div><div> 319 1 1000 1000 1000</div><div> 320 1 1000 1000 1000</div><div> 321 1 1000 1000 1000</div><div> 322 1 1000 1000 1000</div>
<div> 323 1 1000 1000 1000</div><div> 324 1 1000 1000 1000</div><div> 327 1 1000 1000 1000</div><div> 329 1 1000 1000 1000</div><div> 330 1 1000 1000 1000</div><div> 332 1 1000 1000 1000</div>
<div> 333 1 1000 1000 1000</div><div> 335 1 1000 1000 1000</div><div> 337 1 1000 1000 1000</div><div> 338 1 1000 1000 1000</div><div> 341 1 1000 1000 1000</div><div> 342 1 1000 1000 1000</div>
<div> 343 1 1000 1000 1000</div><div> 344 1 1000 1000 1000</div><div> 346 1 1000 1000 1000</div><div> 348 1 1000 1000 1000</div><div> 350 1 1000 1000 1000</div><div> 351 1 1000 1000 1000</div>
<div> 352 1 1000 1000 1000</div><div> 353 1 1000 1000 1000</div><div> 354 1 1000 1000 1000</div><div> 355 1 1000 1000 1000</div><div> 358 1 1000 1000 1000</div><div> 360 1 1000 1000 1000</div>
<div> 361 1 1000 1000 1000</div><div> 363 1 1000 1000 1000</div><div> 364 1 1000 1000 1000</div><div> 366 1 1000 1000 1000</div><div> 367 1 1000 1000 1000</div><div> 368 1 1000 1000 1000</div>
<div> 369 1 1000 1000 1000</div><div> 372 1 1000 1000 1000</div><div> 373 1 1000 1000 1000</div><div> 375 1 1000 1000 1000</div><div> 376 1 1000 1000 1000</div><div> 377 1 1000 1000 1000</div>
<div> 379 1 1000 1000 1000</div><div> 381 1 1000 1000 1000</div><div> 383 1 1000 1000 1000</div><div> 384 1 1000 1000 1000</div><div> 385 1 1000 1000 1000</div><div> 386 1 1000 1000 1000</div>
<div> 387 1 1000 1000 1000</div><div> 388 1 1000 1000 1000</div><div> 391 1 1000 1000 1000</div><div> 393 1 1000 1000 1000</div><div> 394 1 1000 1000 1000</div><div> 396 1 1000 1000 1000</div>
<div> 397 1 1000 1000 1000</div><div> 399 1 1000 1000 1000</div><div> 401 1 1000 1000 1000</div><div> 402 1 1000 1000 1000</div><div> 403 1 1000 1000 1000</div><div> 405 1 1000 1000 1000</div>
<div> 406 1 1000 1000 1000</div><div> 407 1 1000 1000 1000</div><div> 409 1 1000 1000 1000</div><div> 411 1 1000 1000 1000</div><div> 413 1 1000 1000 1000</div><div><br></div></span></div>
<div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif">So how to adjust the force constraint to the harmonic poteitial E = k(r-r0)^2, with different values of k?</font></div><div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif"><br>
</font></div><div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif">I am totally a new user of Gromacs, even MD simulation. Please help, Thanks a lot.</font></div><div><br><div class="gmail_quote">
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Firstly I want to thank for your reply, yes, it should be position restraint.<br>
<br>
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.<br>
<br>
</blockquote>
<br>
Simply reply to the message. The discussion needs to stay on the list. The members are not private tutors.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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,<br>
which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?<br>
<br>
</blockquote>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks, and any helps will be highly appreciated.<br>
<br>
-- <br>
Best,<br>
Liang Liu<br>
</blockquote>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>
</div>