AMBER Archive (2005)

Subject: Re: AMBER: REMD error!!!

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 20 2005 - 10:00:22 CDT

you should manually check that traj file and see what the
problem is. it looks like some sort of file corruption. between
that and the restart problem I wonder if you're having NFS problems,
or disk problems? REMD is more sensitive only because you
are writing to more files, so more chances to have trouble show up.

you're right, without a restart it is very difficult to restart REMD.
We are working on ways to improve this in Amber9.
If you can get your traj files fixed then you can extract coordinates
from those, but it can be tricky to make sure you get a full set for the
same
time point.

Anthony Cruz wrote:

>In this case that the replica 006 restart file is empty that means that the
>restart will be impossible, right??
>
>
>The error of the ptraj is :
>
>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: trajout spcrem_REP.mdcrd.001c
>
>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
> File (spcrem_REP.mdcrd.001c) is an AMBER trajectory (with box info)
>
>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 fix this??? or how I can check the file in this point???
>The set number corresponds to frame???
>
>
>Anthony
>
>
>Anthony
>
>On Thursday 20 October 2005 7:35 am, Carlos Simmerling wrote:
>
>
>>Anthony Cruz wrote:
>>
>>
>>>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...
>>>
>>>
>>the same as any simulation - did it maybe crash while writing?
>>the restart writing is handled the same way for remd as for normal md.
>>make sure you are writing restarts at least once per exchange
>>(make ntwr less than or equal to nstlim)
>>
>>
>>
>>>I fix the ptraj command and I have the same error...
>>>
>>>
>>you can't have the same error, the last error explicitly
>>said that "trjout" was not a valid command. If you fixed it
>>then it must say something different
>>
>>
>>
>>>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???
>>>
>>>
>>yes, the ptraj method that you were trying. I don't know another easy way.
>>
>>
>>
>>>Anthony
>>>
>>>
>>>
>>>u
>>>
>>>
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