AMBER Archive (2005)

Subject: AMBER: REMD error!!!

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Thu Oct 20 2005 - 08:53:18 CDT

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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