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 - 11:49:28 CDT

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 Download prohibited? No problem. CHAT from any browser, without download. Go to http://in.webmessenger.yahoo.com/


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