AMBER Archive (2008)

Subject: AMBER: The list-directed or NAMELIST READ statement cannot be completed

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Thu Jul 17 2008 - 11:42:25 CDT

Hello,
I am trying to do replica exchange calculation using Amber 9.
First of all I am trying to do an equilibration using this input for each
one of my 10 replicas (I only change the temperature from one to another
one):

Equilibration
 &cntrl
        nstlim = 100000, dt = 0.002,
        ntx = 1, temp0 = 300.00, ig=28615,
        gamma_ln = 1.0, ntt = 3,
        ntc = 2, ntf = 2, ntb = 0, nmropt = 1,
        ntwx = 500, ntwr =100000, ntpr = 500,
        cut = 999.0, rgbmax = 999.0,
        nscm = 1000, igb = 5, irest=0,
 &end
 &wt TYPE= END
 /
DISANG=1ftg_dry_chir.dat

As a groupfile I use:

-O -rem 0 -i equilibrate.mdin.001 -o equilibrate.mdout.001 -c min.rst -r
equilibrate.rst.001 -x equilibrate.mdcrd.001 -inf equilibrate.mdinfo.001 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.002 -o equilibrate.mdout.002 -c min.rst -r
equilibrate.rst.002 -x equilibrate.mdcrd.002 -inf equilibrate.mdinfo.002 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.003 -o equilibrate.mdout.003 -c min.rst -r
equilibrate.rst.003 -x equilibrate.mdcrd.003 -inf equilibrate.mdinfo.003 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.004 -o equilibrate.mdout.004 -c min.rst -r
equilibrate.rst.004 -x equilibrate.mdcrd.004 -inf equilibrate.mdinfo.004 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.005 -o equilibrate.mdout.005 -c min.rst -r
equilibrate.rst.005 -x equilibrate.mdcrd.005 -inf equilibrate.mdinfo.005 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.006 -o equilibrate.mdout.006 -c min.rst -r
equilibrate.rst.006 -x equilibrate.mdcrd.006 -inf equilibrate.mdinfo.006 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.007 -o equilibrate.mdout.007 -c min.rst -r
equilibrate.rst.007 -x equilibrate.mdcrd.007 -inf equilibrate.mdinfo.007 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.008 -o equilibrate.mdout.008 -c min.rst -r
equilibrate.rst.008 -x equilibrate.mdcrd.008 -inf equilibrate.mdinfo.008 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.009 -o equilibrate.mdout.009 -c min.rst -r
equilibrate.rst.009 -x equilibrate.mdcrd.009 -inf equilibrate.mdinfo.009 -p
1ftg.dry.top
-O -rem 0 -i equilibrate.mdin.010 -o equilibrate.mdout.010 -c min.rst -r
equilibrate.rst.010 -x equilibrate.mdcrd.010 -inf equilibrate.mdinfo.010 -p
1ftg.dry.top

As, you can see rem 0 means that I am not using replica exchange by now.

I get this error from the calculation, writen a lot of times in the error
file:

1525-049 The list-directed or NAMELIST READ statement cannot be completed
because the input data did not specify a valid delimited character string.
The program will recover by ignoring the item in the READ statement.
(...)
525-049 The list-directed or NAMELIST READ statement cannot be completed
because the input data did not specify a valid delimited character string.
The program will recover by ignoring the item in the READ statement.
[6] MPI Abort by user Aborting program !
[6] Aborting program!
srun: error: s11c4b09: task[0,2]: Exited with exit code 255
srun: error: s11c4b09: task[1,3]: Killed
srun: Job Failed

In the output file I can see:

  Running multisander version of sander amber9
        Group = 4
        Group = 2
        Group = 6
        Group = 8
     Total processors = 20
        WorldRank = 8
        WorldRank = 4
     Number of groups = 10
        NodeID = 0
        NodeID = 0

     Looping over processors:
        WorldRank = 9
        NodeID = 1

        WorldRank = 5
        NodeID = 1

        WorldRank is the global PE rank
        Group = 5
        WorldRank = 10
        NodeID = 0

        Group = 3
        WorldRank = 6
        NodeID = 0

        NodeID is the local PE rank in current group
        WorldRank = 11
        NodeID = 1

        WorldRank = 7
        NodeID = 1

        Group = 0
        WorldRank = 0
        NodeID = 0

        WorldRank = 1
        NodeID = 1

        Group = 1
        WorldRank = 2
        NodeID = 0

        WorldRank = 3
        NodeID = 1

        WorldRank = 12
        NodeID = 0

        WorldRank = 13
        NodeID = 1

        Group = 7
        WorldRank = 14
        NodeID = 0

        WorldRank = 15
        NodeID = 1

        WorldRank = 16
        NodeID = 0

        WorldRank = 17
        NodeID = 1

        Group = 9
        WorldRank = 18
        NodeID = 0

        WorldRank = 19
        NodeID = 1

Could anyone help me to find the reason of this error, please?
Thank you very much in advance for you help.

Best wishes,

Rebeca García Fandiño
Parc Cientific de Barcelona
Universidad de Barcelona
Spain
rebeca_at_mmb.pcb.ub.es

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