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 - 13:04:26 CDT

I have amber9 version installed on clusters and Amber10 is not available in the institute at present. I have not send you the complete group file, but shown command line for one of the replica. ----- Original Message ---- From: Carlos Simmerling <carlos.simmerling_at_gmail.com> To: amber_at_scripps.edu Sent: Thursday, 25 September, 2008 11:21:58 PM Subject: Re: AMBER: error while running REMD in amber9 ok but I don't understand how it works with the groupfile that you sent. maybe here there was just some error in the filesystem and it could not read the data. try restarting (this is much easier in amebr10, I suggest upgrading if you are running REMD) On Thu, Sep 25, 2008 at 1:44 PM, priya priya <priyaanand_27_at_yahoo.co.in> wrote: > 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 > > ________________________________ > 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 Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
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