Re: smd dimer dissociation

From: Pawel Weronski (
Date: Wed Apr 26 2006 - 14:12:45 CDT

Dear Jerome,

I have used adaptive biasing force (ABF) method to estimate the change
of the free energy corresponding to adsorption of a peptide nucleic acid
(PNA) molecule to a lipid (POPC) - water interface. I equilibrated my
system for several hundreds of nanoseconds and I see that my PNA
molecule is attached to the interface. Even more, hydrophobic parts of
the molecule are a little "immersed" in the non-polar internal part of
the bilayer. Now, I am trying to pull off the molecule back to the water
phase to calculate the change of the free energy of the process. Because
both the PNA molecule and the lipid bilayer are relatively "soft"
structures, I have used harmonic restraints to avoid their deformation,
which would of course change the calculated free energy value. I fixed
positions of all my N and P1 atoms on one side of the bilayer using the
constraint "harm" and the force constants fx=fy=fz=50. I also
constrained the conformation of the PNA molecule using the constraint
"dist" between its atoms and the same value of the force constant. My
simulations run fine as long as they are not canceled, what
unfortunately occurs at each 10 hours (that is how our allocations are
technically organized). When I try to restart I get one of two error
messages. Usually it is:

ERROR: Constraint failure in RATTLE algorithm for atom 7466!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.

and these messages are written to my simulation log file. Of course the
atom index (7466) changes from one cancellation to another. Sometimes, I
get a message in my error file:

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: domain error: argument not in valid range
    while executing
"expr [lindex $coords($g2) 2] - [lindex $coords($g1) 2"
    (in namespace eval "::ABF::ABFcoord" script line 5)
    invoked from within
"namespace eval ABFcoord {

    loadcoords coords

    return [expr [lindex $coords($g2) 2] - [lindex $coords($g1) 2]]
    (procedure "ABFcoord" line 2)
    invoked from within
    (in namespace eval "::ABF" script line 52)
    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

MPI: On host, Program /scratch/pawel/1pupa1/namd2, Rank
0, Process 5798 called MPI_Abort(<communicator>, 1)

MPI: --------stack traceback-------
sh: line 1: idb: command not found

MPI: -----stack traceback ends-----
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job

Do you have an idea what I can do to be able to restart my simulations?
I have also done very similar simulations with another PNA molecule that
has had no hydrophobic parts (no parts immersed in the organic phase). I
saw a similar behavior when the molecule was near the interface, but it
occurred relatively seldom.

Thanks for your help,


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