<br clear="all">> Date: Thu, 19 Mar 2009 13:52:09 +0800<br>> From: huifang liu <<a href="mailto:huifangliu1985@gmail.com">huifangliu1985@gmail.com</a>><br>> Subject: [gmx-users] how to get the the force plot after pulling<br>
> dynamic simulation using GMX-3.3<br>> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Message-ID:<br>> <<a href="mailto:e523c6be0903182252i114666bam4bbe591a10a30677@mail.gmail.com">e523c6be0903182252i114666bam4bbe591a10a30677@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>><br>> I am recently doing a SMD. I think i did it very well. But i don't know how<br>> to get the force plot. Is there some one can give me a suggestion?<br>
> Thank you very much.<br>><br>At the end of the SMD you should have obtained a .pdo file. In that file<br>the time and the coordinates of the reference- (R), pull-group (P) and<br>of the spring (S) are written. If i remember correctly it was: t, Rx,<br>
Ry, Rz, Px, Sx, Py, Sy, Pz, Sz. If you have more pullgroups then you<br>have first the x-coordinates of P and S, then y-coordinates ... (look in<br>the manual or the header of the .pdo; or for t=0 you should know the<br>position of all particals and springs and can calculate a little bit to<br>
see which entry corresponds to which group).
<div> </div>
<div>
<div>Hi, Thomas, </div>
<div> </div>
<div>Thank you very much for your reply. It is really helpful to me. But there are two things that still confuse me.</div>
<div>My .pdo file is like this:</div>
<div># AFM 3.0<br># Component selection: 1 1 1<br># nSkip 1<br># Ref. Group 'USK'<br># Nr. of pull groups 1<br># Group 1 'UNK' afmVec -0.179258 0.695867 -0.695439 AfmRate 0.005000 AfmK 500.000000<br>
#####<br>0.000000 2.739100 6.984308 2.668408 4.016277 4.016280 2.026386 2.026388 7.623277 7.623278<br>0.002000 2.739100 6.984308 2.668408 4.016277 4.016278 2.026386 2.026394 7.623277 7.623271<br>
0.004000 2.739100 6.984308 2.668408 4.016277 4.016276 2.026386 2.026401 7.623277 7.623264<br>0.006000 2.739100 6.984308 2.668408 4.016277 4.016275 2.026386 2.026408 7.623277 7.623257<br>
0.008000 2.739100 6.984308 2.668408 4.016277 4.016273 2.026386 2.026415 7.623277 7.623250<br>0.010000 2.739100 6.984308 2.668408 4.016277 4.016271 2.026386 2.026422 7.623277 7.623243<br>
0.012000 2.739100 6.984308 2.668408 4.016277 4.016269 2.026386 2.026429 7.623277 7.623236<br>0.014000 2.739100 6.984308 2.668408 4.016277 4.016267 2.026386 2.026436 7.623277 7.623229<br>
0.016000 2.739100 6.984308 2.668408 4.016277 4.016266 2.026386 2.026443 7.623277 7.623222<br>0.018000 2.739100 6.984308 2.668408 4.016277 4.016264 2.026386 2.026450 7.623277 7.623215<br>
0.020000 2.739100 6.984308 2.668408 4.016277 4.016262 2.026386 2.026457 7.623277 7.623208<br>0.022000 2.739100 6.984308 2.668408 4.016277 4.016260 2.026386 2.026464 7.623277 7.623201<br>
</div>
<div>Since the column 5, 7, 9 only changed after every picosecond and column 6, 8,10 changed per 0.002 ps (i set the dt=0.002 in .mdp file). I am wondering whether the column 5,7,9 stand for Sx, Sy, Sz or Px, Py, Pz as you said. If you are right, why the Px, Py, Pz keep the same every picosecond? Is this beacuse that i set the nstxout=500 in the .mdp file (1ps=dt*nstxout). </div>
</div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br>For the force-calculation: The force is the deflection of the spring<br>times the force-constant of the spring -> Fx = k(Sx-Px) ... for the<br>
other directions it's analog. Then you can calculate the magnitude of F<br>and plot it against the time (if you are only interested in the<br>magnitude of force). Or you can calculate the force in the pulling<br>direction and plot it against time.</blockquote>
<div>If i want to calcutate the force in the pulling direction, F=sqrt(Fx*Fx+Fy*Fy+Fz*Fz) ?</div>
<div> </div>
<div>Thank you so much.</div>
<div> </div>
<div>Huifang</div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br><br>Hope this helps.<br>Thomas</blockquote>
<div> </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br>> Huifang<br>><br>> --<br>> Huifang Liu (Ph.D. Student)<br>> School of Pharmacy<br>
> Fudan University<br>><br>> 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)<br>> Shanghai, China, 200032 Cell phone: +86-13764669357<br>> E-mail: <a href="mailto:huifangliu1985@gmail.com">huifangliu1985@gmail.com</a> Fax: (86-21)54237264<br>
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><br><br>-- <br>Huifang Liu (Ph.D. Student)<br>School of Pharmacy<br>Fudan University<br><br>138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)<br>Shanghai, China, 200032 Cell phone: +86-13764669357<br>E-mail: <a href="mailto:huifangliu1985@gmail.com">huifangliu1985@gmail.com</a> Fax: (86-21)54237264<br>
</blockquote>