AMBER Archive (2008)

Subject: Re: AMBER: error while running REMD in amber9

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 24 2008 - 13:27:22 CDT

can you send your sander script? unit 9 should be in inpcrd file.
I would take a look at your files and see if something got corrupted,
or if the disk is full, or your quota full, or something like that.

On Wed, Sep 24, 2008 at 1:53 PM, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
> Dear All,
> I am running REMD for a peptide system, but after running for 70ns it is
> showing some errors, I am not able to make out what is going wrong from the
> error shown below.
> forrtl: severe (24): end-of-file during read, unit 9, file
> /direct/home/test/artic_rem_90ns.out.rep10
> Image PC Routine Line Source
> sander.MPI 000000000081CDA3 Unknown Unknown Unknown
> sander.MPI 000000000081B282 Unknown Unknown Unknown
> sander.MPI 00000000007F06AA Unknown Unknown Unknown
> sander.MPI 00000000007AFE22 Unknown Unknown Unknown
> sander.MPI 00000000007AFA83 Unknown Unknown Unknown
> sander.MPI 00000000007C9326 Unknown Unknown Unknown
> sander.MPI 00000000004FCF00 Unknown Unknown Unknown
> sander.MPI 00000000004B7C60 Unknown Unknown Unknown
> sander.MPI 00000000004B3A8E Unknown Unknown Unknown
> sander.MPI 000000000040436A Unknown Unknown Unknown
> libc.so.6 00002B79AF707154 Unknown Unknown Unknown
> sander.MPI 00000000004042A9 Unknown Unknown Unknown
>
> My input file is as below:
> &cntrl
> imin = 0, nstlim=100, dt=0.002,gbsa =1,surften=0.005,
> ntx = 5, tempi =325.7, temp0 =325.7,
> ntt = 3, tol = 0.0000001,
> ntc = 2, ntf = 2, ntb =0,
> ntwx = 100, ntwe = 500, ntwr = 100, ntpr = 100,
> cut =15.0, scee = 1.2, ibelly =0,
> ntr = 0, gamma_ln = 5.0,offset = 0.09
> nscm = 500, igb = 1,
> irest = 1,numexchg = 150000, repcrd = 0,ntave = 0,
> /
>
> Please suggest
>
> Regards
> Priya
>
> ________________________________
> Unlimited freedom, unlimited storage. Get it now
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