Date: Wed, 23 May 2007 02:29:36 -0700From: [EMAIL PROTECTED]: [EMAIL
PROTECTED]: [gmx-users] Restarting AFM pulling
Hello everyone,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.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.The end of the .pdo from the first run
looks like this:...12.000001
4.537002 1.228887 1.279260I 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).And in the beginning of the new run I get:Hello
Everybody,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.In the code md.c in the funtion
:pull(&pulldata,state->x,f,force_vir,state->box,
top,inputrec->delta_t,step,t, mdatoms,START(nsb),HOMENR(nsb),cr);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:In do_afm();for(m=0;m<DIM;m++)
pull->grp[i].spring[m] = pull->grp[i].AfmInit[m] + pull->ref.x_unc[m] +
pull->grp[i].AfmVec[m]*pull->grp[i].AfmRate*step*dt;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.I reported the bug at:http://www.pku.edu.cn/ehomepage.htmgreetings,Jiang,
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