There is disk space in the cluster.
I am already running REMD for different systems, all are running fine, but this simulation ended after running 54ns, showing that error.
----- Original Message ----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
To: amber.scripps.edu
Sent: Thursday, 25 September, 2008 10:25:35 PM
Subject: Re: AMBER: error while running REMD in amber9
did the test case work? you might want to follow the format for the
groupfile given in the test case- I'm not sure how this one could have
worked at all. also, did you check your disk as I suggested?
On Thu, Sep 25, 2008 at 12:49 PM, priya priya <priyaanand_27.yahoo.co.in> wrote:
> Dear Sir,
>
> inpcrd file is attached with the mail, and the script i used in groupfile
> is:
>
> $AMBERHOME/exe/sander.MPI -O -rem 1 -remlog rem.log -i rem.in.1 -p
> artic.prmtop -inf rem_50ns.reminforep1 -o rem_50ns.out.rep1 -c
> rem_35ns.rst.rep1 -r rem_50ns.rst.rep1 -x rem_50ns.mdcrd.rep1
>
>
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: amber.scripps.edu
> Sent: Wednesday, 24 September, 2008 11:57:22 PM
> Subject: Re: AMBER: error while running REMD in amber9
>
> 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.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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Received on Fri Sep 26 2008 - 05:11:21 PDT
