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<br><br><blockquote><hr>Date: Wed, 23 May 2007 02:29:36 -0700<br>From: yesint4@yahoo.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Restarting AFM pulling<br><br>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Hello everyone,<br>I'me trying to run a very long simulation with the AFM pulling, which should be partitioned into many smaller pieces. However, this seems that the pull code does not preserve the force even if the position of the spring is set to what was observed at the end of the previous run.<br>Here is an example. I have one pull group pulled in Z direction, so in the .pdo file, according to the manual, I have the time, the position of the reference, the position of the pull group and the pos. of the spring.<br>The end of the .pdo from the first run looks like this:<br><br>...<br>12.000001
4.537002 1.228887 1.279260<br><br>I start new run with the afm_init1 = 0 0 -3.257742 (the last number is 1.279260-4.537002 i.e. relative pos. of the spring as it should be).<br>And in the beginning of the new run I get:<br><br>Hello Everybody,<br>I just red the email of mister Semen and I indeed found a bug in the pull code. I allready checked it together with my professor and could duplicate both error and prove solution.<br>In the code md.c in the funtion :<br><br>pull(&pulldata,state->x,f,force_vir,state->box,<br> top,inputrec->delta_t,step,t,<br> mdatoms,START(nsb),HOMENR(nsb),cr);<br><br>The integer parameter is step incorrect incase of continuation of the run, step has to be equal to step_rel instead of step. Otherwise the following equation in pull.c is not correct:<br>In do_afm();<br><br>for(m=0;m<DIM;m++)<br> pull->grp[i].spring[m] = pull->grp[i].AfmInit[m] + pull->ref.x_unc[m] +<br> pull->grp[i].AfmVec[m]*pull->grp[i].AfmRate*step*dt;<br><br>As pull->grp[i].AfmInit[m] is reset, step isn't. In case of resubmitting the occurring error scales with rate and the length of the run. The same error in the constraint part in pull.c.<br><br>I reported the bug at:<br>http://www.pku.edu.cn/ehomepage.htm<br><br>greetings,<br><br>Jiang,<br><br><br><br><br><br><br></div></div></div><br>
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