AMBER Archive (2005)

Subject: Re: Re: AMBER: REMD error!!!

From: Melinda Layten (mlayten_at_gmail.com)
Date: Fri Oct 28 2005 - 10:26:46 CDT

If you have a text trajectory and a water box, at the end of each frame is a
3 field line with coordinates of the box, the previous line may also be
shorter then standard lines.

On 10/28/05, Anthony Cruz <acb15885_at_uprm.edu> wrote:
>
> I have a little question. How I can identify frames in the trajectory
> file?
> What separate the frame??? Because I want to try to recuperate some of the
> trajectory files from my REMD That are corrupted.
>
> Thank you all.
> Anthony
>
> ---------- Forwarded Message ----------
>
> Subject: Re: AMBER: REMD error!!!
> Date: Thursday 20 October 2005 1:13 pm
> From: Anthony Cruz <acb15885_at_uprm.edu>
> To: amber_at_scripps.edu
>
> Thank you to ALL for your answers.
>
> I think that is something wrong with the file because at frame 2300 the
> file
> have only 32M. I will truncate the file after this point.
> Thank you for all your help!
>
> Anthony
>
> On Thursday 20 October 2005 10:28 am, Carlos Simmerling wrote:
> > would the 2GB limit really cause it to stop at frame 2300?
> > maybe- that's why I suggested manual inspection.
> > Still, it seems like it should read the first 2GB and
> > unless his system is huge that should be more than 2300 frames.
> > carlos
> >
> > Wei Zhang wrote:
> > >Hi Anthony:
> > >
> > >The ptraj error is because your trajectory file exceed 2G limit which
> is
> > >beyond the limitation of ptraj. To fix this you need to manually change
> > >the makefile add
> > >
> > >-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
> > >
> > >to CFLAG and recompile ptraj, this may solve your problem
> > >
> > >On Thu, 2005-10-20 at 07:53 -0600, Anthony Cruz wrote:
> > >>Hi User:
> > >>
> > >>I was doing a Replica exchange dynamics simulation of a small peptide
> > >> with 16 temperature. The simulation stop before it ends. I have the
> > >> following information from PBS:
> > >>
> > >>***************
> > >>logfile (*.log)
> > >>***************
> > >> RUNNING MULTISANDER VERSION OF SANDER AMBER8
> > >> Total processors = 16
> > >> Number of groups = 16
> > >>
> > >> Looping over processors:
> > >> WorldRank is the global PE rank
> > >> NodeID is the local PE rank in current group
> > >>
> > >> Group = 0
> > >> WorldRank = 0
> > >> NodeID = 0
> > >>
> > >> Group = 1
> > >> WorldRank = 1
> > >> NodeID = 0
> > >>
> > >> Group = 2
> > >> WorldRank = 2
> > >> NodeID = 0
> > >>
> > >> Group = 3
> > >> WorldRank = 3
> > >> NodeID = 0
> > >>
> > >> Group = 4
> > >> WorldRank = 4
> > >> NodeID = 0
> > >>
> > >> Group = 5
> > >> WorldRank = 5
> > >> NodeID = 0
> > >>
> > >> Group = 6
> > >> WorldRank = 6
> > >> NodeID = 0
> > >>
> > >> Group = 7
> > >> WorldRank = 7
> > >> NodeID = 0
> > >>
> > >> Group = 8
> > >> WorldRank = 8
> > >> NodeID = 0
> > >>
> > >> Group = 9
> > >> WorldRank = 9
> > >> NodeID = 0
> > >>
> > >> Group = 10
> > >> WorldRank = 10
> > >> NodeID = 0
> > >>
> > >> Group = 11
> > >> WorldRank = 11
> > >> NodeID = 0
> > >>
> > >> Group = 12
> > >> WorldRank = 12
> > >> NodeID = 0
> > >>
> > >> Group = 13
> > >> WorldRank = 13
> > >> NodeID = 0
> > >>
> > >> Group = 14
> > >> WorldRank = 14
> > >> NodeID = 0
> > >>
> > >> Group = 15
> > >> WorldRank = 15
> > >> NodeID = 0
> > >>
> > >>getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
> > >>
> > >>
> > >>************
> > >>error (*.e)
> > >>************
> > >>forrtl: severe (24): end-of-file during read, unit 9,
> > >>file /home/asantana/asv.299/spcrem_REP.rst.006
> > >>Image PC Routine Line
> > >> Source sander.REM 400000000049E880 Unknown
> > >> Unknown Unknown sander.REM 400000000049D990 Unknown
> > >> Unknown Unknown sander.REM 4000000000455EE0 Unknown
> > >> Unknown Unknown sander.REM 40000000003C5140 Unknown
> > >> Unknown Unknown sander.REM 40000000003C60B0 Unknown
> > >> Unknown Unknown sander.REM 40000000003F7220
> > >> Unknown Unknown Unknown sander.REM
> > >> 400000000011CA70 Unknown Unknown Unknown sander.REM
> > >> 400000000007DD60 Unknown Unknown Unknown sander.REM
> > >> 4000000000078AC0 Unknown Unknown Unknown
> > >> sander.REM 40000000000052D0 Unknown Unknown
> > >> Unknown libc.so.6.1 2000000000666990 Unknown
> > >> Unknown Unknown sander.REM 4000000000004CC0 Unknown
> > >> Unknown Unknown MPI: MPI_COMM_WORLD rank 6 has terminated without
> > >> calling MPI_Finalize() MPI: aborting job
> > >>
> > >>What could be the problem???
> > >>Can I restart this simulation?
> > >>
> > >>Also when I try to truncate the trajectory the process stop with the
> > >> following error:
> > >>
> > >>Amber8 Module: ptraj
> > >>
> > >>Read in control variables
> > >>Read in atom names...
> > >>Read in charges...
> > >>Read in masses...
> > >>Read in IAC (atoms involved in L-J)...
> > >>Read in NUMEX (index to excl atom list)...
> > >>Read in NNO (index for nonbond of @type)...
> > >>Read in residue labels...
> > >> LEU ARG ILE PRO CYS CYS PRO VAL ASN LEU
> > >> LYS ARG LEU LEU VAL VAL VAL VAL VAL VAL
> > >> VAL LEU VAL VAL VAL VAL ILE VAL GLY ALA
> > >> LEU LEU MET GLY LEU
> > >>Read in the residue to atom pointer list...
> > >>Read in bond parameters RK and REQ...
> > >>Read in angle parameters TK and TEQ...
> > >>Read in dihedral parameters PK, PN and PHASE...
> > >>Read in SOLTY...
> > >>Read in L-J parameters CN1 and CN2...
> > >>Read in info for bonds w/ hydrogen...
> > >>Read in info for bonds w/out hydrogen...
> > >>Read in info for angles w/ hydrogen...
> > >>Read in info for angles w/out hydrogen...
> > >>Read in info for dihedrals w/ hydrogen...
> > >>Read in info for dihedrals w/out hydrogen...
> > >>Read in excluded atom list...
> > >>Read in h-bond parameters: AG, BG, and HBCUT...
> > >>Read in atomic symbols (types)...
> > >>Read in tree information...
> > >>Read in the JOIN info...
> > >>Read in the IROTAT info...
> > >>Successfully completed readParm.
> > >>
> > >>PTRAJ: Processing input file...
> > >> Input is from standard input
> > >>
> > >>PTRAJ: trajin spcrem_REP.mdcrd.001 1 167675
> > >>Checking coordinates: spcrem_REP.mdcrd.001
> > >>FYI ptraj(): trajin stop value (167675) is greater than the number of
> > >> sets read in
> > >>FYI ptraj(): Setting stop to the maximum value (167673)
> > >>
> > >>PTRAJ: trjout spcrem_REP.mdcrd.001c
> > >>
> > >>ERROR in dispatchToken: Token string "trjout" not found in tokenlist
> > >>
> > >>
> > >>ERROR in dispatchToken: Token string "spcrem_rep.mdcrd.001c" not found
> in
> > >>tokenlist
> > >>
> > >>FYI: No output trajectory specified (trajout), none will be saved.
> > >>
> > >>PTRAJ: Successfully read the input file.
> > >> Coordinate processing will occur on 167673 frames.
> > >> Summary of I/O and actions follows:
> > >>
> > >>INPUT COORDINATE FILES
> > >> File (spcrem_REP.mdcrd.001) is an AMBER trajectory with 167673 sets
> > >>
> > >>OUTPUT COORDINATE FILE
> > >> NULL entry
> > >>
> > >>ACTIONS
> > >> Stack is NULL
> > >>
> > >>Processing AMBER trajectory file spcrem_REP.mdcrd.001
> > >>
> > >>Set 1 .................................................
> > >>Set 50 .................................................
> > >>Set 100 .................................................
> > >>Set 150 .................................................
> > >>Set 200 .................................................
> > >>Set 250 .................................................
> > >>Set 300 .................................................
> > >>Set 350 .................................................
> > >>Set 400 .................................................
> > >>Set 450 .................................................
> > >>Set 500 .................................................
> > >>Set 550 .................................................
> > >>Set 600 .................................................
> > >>Set 650 .................................................
> > >>Set 700 .................................................
> > >>Set 750 .................................................
> > >>Set 800 .................................................
> > >>Set 850 .................................................
> > >>Set 900 .................................................
> > >>Set 950 .................................................
> > >>Set 1000 .................................................
> > >>Set 1050 .................................................
> > >>Set 1100 .................................................
> > >>Set 1150 .................................................
> > >>Set 1200 .................................................
> > >>Set 1250 .................................................
> > >>Set 1300 .................................................
> > >>Set 1350 .................................................
> > >>Set 1400 .................................................
> > >>Set 1450 .................................................
> > >>Set 1500 .................................................
> > >>Set 1550 .................................................
> > >>Set 1600 .................................................
> > >>Set 1650 .................................................
> > >>Set 1700 .................................................
> > >>Set 1750 .................................................
> > >>Set 1800 .................................................
> > >>Set 1850 .................................................
> > >>Set 1900 .................................................
> > >>Set 1950 .................................................
> > >>Set 2000 .................................................
> > >>Set 2050 .................................................
> > >>Set 2100 .................................................
> > >>Set 2150 .................................................
> > >>Set 2200 .................................................
> > >>Set 2250 .................................................
> > >>Set 2300 .................................................
> > >>Set 2350 ...................................
> > >>ERROR in readAmberTrajectory(): Set #2386 is corrupted ( 4.066 2)...
> > >>
> > >>
> > >>
> > >>PTRAJ: Successfully read in 2385 sets and processed 2385 sets.
> > >> Dumping accumulated results (if any)
> > >>
> > >>How I can repair the data???
> > >>I going to loose all the work???
> > >>
> >
> >>-----------------------------------------------------------------------
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>
>
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