AMBER Archive (2005)

Subject: Re: AMBER: REMD error!!!

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Thu Oct 20 2005 - 09:45:32 CDT

Thank you Carlos.
The spcrem_REP.rst.006 file is empty!!!
which could be the reason for this. This will make impossible the restart of
the simulation...

I fix the ptraj command and I have the same error...

I can load the file in vmd because the file has 2.2G . Exist any form to
reduce the size of the file to load it in vmd???

Anthony

On Thursday 20 October 2005 6:05 am, Carlos Simmerling wrote:
> 1) check your restart file
>
> spcrem_REP.rst.006 visually (using vi or a text editor).
>
> does it look ok? any corrupted lines, or ***, or something else
> wrong? Can you load that coordinate file into a program like VMD?
>
> 2) the command for ptraj is trajout, not trjout. Fix that and rerun it.
>
> 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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