From: Jiang ran <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: [gmx-users] BUG!!! AFM pulling/Constraint
Date: Thu, 24 May 2007 21:56:18 +0800
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,
You are right.
But in the current pull code there is no real solution to this problem,
since the initial position of the spring is set to the pull group position,
which is not equal to the position of the spring at the end of the previous
run.
There are many more problem in the pull code in 3.3.1 (and before).
For 4.0 I have completely rewritten the pull code, so (nearly) all problems
should be solved then.
Berk.
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