Re: ABF Simulation

From: Lionel Perrin (lionel.perrin_at_cea.fr)
Date: Wed Nov 02 2005 - 08:28:25 CST

Hi Jerome,

thank's lot once more, the simulation is now running with your modified
vectors.tcl.
I will tell you the outcome of this try.

all the best,

Lionel

Le ven 28/10/2005 à 11:05, Jérôme Hénin a écrit :
> Lionel, Jim,
>
> I discussed the issue with a few core Tcl developpers. This seems to be
> related to corrupted data ending up in the variables used by ABF. As one of
> these people put it: "something out-of-thread is fouling your state". Jim, do
> you have any idea where this could come from?
>
> You'll notice that these errors appear in the vector routines defined in
> vector.tcl, which is borrowed to VMD. In that file, expr statements are not
> protected by curly braces. The Tcl guys recommend that the arguments to expr
> always be enclosed in braces. Doing this might prevent crashes, but if the
> data is really corrupted, I suppose some erroneous behavior is to be expected
> anyway.
>
> Lionel, I attach a version of vectors.tcl with curly braces inserted where
> applicable, so that you can try and see if it solves anything.
>
> Jerome
>
>
> On Wednesday 26 October 2005 17:52, Lionel Perrin wrote:
> > Jerome,
> >
> > I have changed the indexes and restarted the simulation,
> > after 1.6ns of propagation, I got a floating-point error :
> >
> > WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1618000
> > WRITING COORDINATES TO DCD FILE AT STEP 1618000
> > WRITING COORDINATES TO RESTART FILE AT STEP 1618000
> > FINISHED WRITING RESTART COORDINATES
> > WRITING VELOCITIES TO RESTART FILE AT STEP 1618000
> > FINISHED WRITING RESTART VELOCITIES
> > LDB: LOAD: AVG 12.143 MAX 12.3366 MSGS: TOTAL 78 MAXC 12 MAXP 4 None
> > LDB: LOAD: AVG 12.143 MAX 12.3366 MSGS: TOTAL 78 MAXC 12 MAXP 4
> > Refine
> > TCL: unknown floating-point error, errno = 4
> > FATAL ERROR: unknown floating-point error, errno = 4
> > while executing
> > "expr -$i"
> > (procedure "vecinvert" line 4)
> > invoked from within
> > "vecinvert $F2"
> > (in namespace eval "::ABF::ABFcoord" script line 12)
> > invoked from within
> > "namespace eval ABFcoord {
> >
> > set dr [vecsub $coords($abf2) $coords($abf1)]
> > set r [veclength $dr]
> > set nv [vecnorm $dr] ;# unity vector abf1 -> abf2
> >
> > ..."
> > (procedure "ABFapply" line 5)
> > invoked from within
> > "ABFapply $F"
> > (in namespace eval "::ABF" script line 84)
> > invoked from within
> > "namespace eval ::ABF {
> >
> > # First timestep : we don't have forces
> > if { $timestep == 0 } {
> >
> > # must not be equal to $timestep - 1
> > set timeStored -2
> > ..."
> > (procedure "calcforces" line 2)
> > invoked from within
> > "calcforces"
> >
> > here is my ABF input section (the rest of my input has remained
> > unchanged with respect to my previous trials) :
> >
> > source /usr/local/NAMD_2.6b1_Linux-i686/lib/abf/abf.tcl
> > abf coordinate distance
> > abf abf1 2472
> > abf abf2 3233
> > abf ximin 3.0
> > abf ximax 13.0
> > abf dxi 0.1
> > abf dsmooth 0.2
> > abf forceconst 10.0
> > abf fullsamples 500
> > abf outfile 1J8A_abf.abf
> > abf historyfile 1J8A_abf.his
> > abf outputfreq 5000
> > abf writexifreq 1000
> > abf distfile 1J8A_abf.dis
> >
> > sincerly,
> >
> > Lionel
> >
> > Le ven 21/10/2005 à 11:03, Lionel Perrin a écrit :
> > > Jerome,
> > >
> > > Thank you for the answer, I knew about the index issue between NAMD and
> > > VMD but I did not pay attention that time ! :-S
> > > I have restarted the simulation with the "good" indexes and will tell
> > > you the outcome of the ABF simulation.
> > >
> > > thank's a lot,
> > >
> > > Lionel
> > >
> > > Le mer 19/10/2005 à 11:11, Jérôme Hénin a écrit :
> > > > Lionel,
> > > >
> > > > I believe that part of the problem lies in the atom indexes you pass to
> > > > ABF when defining the reaction coordinate. Your files indicate that you
> > > > are using atom indexes given by VMD, which start at 0. However, NAMD
> > > > uses the PDB convention for atom indexes, which starts at 1, so the
> > > > atoms you pass to ABF are not the ones you intended. This is a very
> > > > common pitfall that probably deserves to be more publicized in the
> > > > community of NAMD+VMD users.
> > > >
> > > > I don't have a clear idea of why you get that Tcl floating-point error,
> > > > though. Since one of the atoms is a hydrogen, it might be more prone to
> > > > numerical instability than a heavy atom, but this is not really a
> > > > satisfactory explanation to me. And since you are not constraining
> > > > protein hydrogens, issues involving constraints can be ruled out.
> > > >
> > > > If anyone else experiences similar crashes, please tell me about it!
> > > >
> > > > Jerome
> > > >
> > > > On Thursday 06 October 2005 16:13, Lionel Perrin wrote:
> > > > > Chris,
> > > > >
> > > > > The two atoms defining the reaction coordination belong to two
> > > > > distinct molecules, X1 corresponds to the Cgamma of an aspartate and
> > > > > X2 corresponds to the C atom of the amidine function of a ligand.
> > > > > Hence, these two centers are not "chemically" bonded.
> > > > >
> > > > > In this case, should I apply a force constant at the border of the
> > > > > reaction coordinate and/or and external restraint ?
> > > > >
> > > > > Lionel
> > > > >
> > > > > Le mer 05/10/2005 à 14:58, Chris Chipot a écrit :
> > > > > > Lionel,
> > > > > >
> > > > > > could you tell us what atoms are involved in your reaction
> > > > > > coordinate ? Are these atoms chemically bonded to constrained
> > > > > > degrees of freedom ?
> > > > > >
> > > > > >
> > > > > > Chris Chipot

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