Re: ABF Simulation

From: Lionel Perrin (lionel.perrin_at_cea.fr)
Date: Wed Oct 26 2005 - 10:52:53 CDT

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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