[gmx-users] BUG!!! AFM pulling/Constraint

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 24 16:10:16 CEST 2007

Jiang ran wrote:
>     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.htm
>     greetings,
>     Jiang,

OK that looks useful, please submit a bugzilla (link from GROMACS
homepage) so the development crew know where to find it when they have
time to fix it.


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