AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 17 2008 - 11:47:24 CDT

some computers are very picky about the namelist format.
this style works for me, while others did not on this machine
and gave namelist errors. try something similar, paying attention
to the format of the last few lines:

mdin
 &cntrl
  imin = 0, nstlim = 50, dt = 0.001,
  ntx = 1, irest = 0, temp0 = 325.0, tempi=325.,
  ntt = 3, tol = 0.000001, gamma_ln=1.,
  ntc = 2, ntf = 1, ntb = 0,
  ntwx = 1000, ntwr = 1000, ntpr = 1,
  scee = 1.2, cut = 99.0, cut_inner = 15,
  nscm = 500, igb = 5, nrespa=4, nrespai=2,
  ig = 18345,
  nmropt=1,
 /
 &wt
  TYPE='END',
 /
DISANG=./disang3

On Thu, Jul 17, 2008 at 12:42 PM, rebeca <rebeca_at_mmb.pcb.ub.es> wrote:
> 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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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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