AMBER Archive (2008)

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

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Thu Sep 25 2008 - 12:44:13 CDT

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_at_gmail.com> To: amber_at_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_at_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_at_gmail.com> > To: amber_at_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_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 > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" (in the *body* of the email) > to majordomo_at_scripps.edu > > ________________________________ > Did you know? You can CHAT without downloading messenger. Click here ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo_at_scripps.edu Did you know? You can CHAT without downloading messenger. Go to http://in.webmessenger.yahoo.com/
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