do you have a lot of experience running MD? I'm just checking to see
the best way to help you out. Why are you running GB solvation on
a system with explicit water? If that is what you want then it can be ok,
but
that is a very advanced technique. REMD can go very wrong if you are
not already an expert with normal MD.
Also if it doesn't work with normal MD either then it is not a problem with
REMD,
you might get better response by sending a new mail to the list saying that
MD doesn't work and not limiting it to the people who understand REMD.
You might try to compare your mdin files that do/do not work and try
changing
things one at a time until you narrow down what is causing the problem,
and then mailing the list again with a more specific request.
good luck
On 6/18/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
> no i tried with different mdin, but if i try running md using this mdin
> (except numexchange) it is giving the same error in the output file ,Error: ifbox=2 in prmtop but angles are not correct.
> Yes, i am using the different inpcrd files for different replicas as they
> are generated by running NVT and NPT on solvated peptide, at their
> respective temperature.
> I am using igb=1
> prmtop and inpcrd was created using xleap after adding TIP3PBOX using an
> octahedron box of size 9.
>
>
> *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
>
> and you used EXACTLY the same mdin (except numexchg)?
> the same inpcrd and prmtop as well? are you using different
> inpcrd for different replicas?
>
> I'm just checking since the simulation is GB (igb=1) but
> sander says that you have a prmtop with periodic box.
> maybe it would help if you tell us about the box info as
> far as how you built the system in leap.
>
>
> On 6/18/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
> >
> > simple MD is running but REM is not,
> > the error :Error: ifbox=2 in prmtop but angles are not correct,
> > says that the rst and prmtopp files box doen't match each other.
> > What should i do
> >
> > REgards'
> >
> > *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
> >
> > can you run normal MD starting with the same inpcrd and prmtop?
> >
> > On 6/18/07, priya priya <priyaanand_27.yahoo.co.in > wrote:
> > >
> > > Dear all
> > >
> > > i am facing problem running rem on amber9.when i submit my job it
> > > gives an error in output file:
> > >
> > > Error: ifbox=2 in prmtop but angles are not correct
> > >
> > > *** input error(s)
> > >
> > > MY input file is as follows:
> > >
> > > am15.in - igb = 0
> > > &cntrl
> > > imin = 0, nstlim = 10000, dt = 0.002,
> > > ntx = 5, temp0 = 273.0,
> > > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > > ntwx = 500, ntwe = 500, ntwr = 500, ntpr = 500,
> > > scee = 1.2, cut = 99.0,
> > > ntr = 0, tautp = 0.1, offset = 0.09,
> > > nscm = 500, igb = 1, numexchg = 40000,
> > > irest = 1, ntave = 0,
> > > and in th error file it gives that :
> > >
> > > [7] MPI Abort by user aborting program !
> > > PSE: [7(5483)] Aborting program
> > > PSE: [7]: Killing all processes, reason: Abort
> > >
> > > forrtl: error (78): process killed (SIGTERM)
> > > forrtl: error (78): process killed (SIGTERM)
> > > PSIlogger: Child with rank 6 exited with status 1.
> > > [4] MPI Abort by user aborting program !
> > > PSE: [4(5470)] Aborting program
> > > PSE: [4]: Killing all processes, reason: Abort
> > > PSIlogger: Child with rank 7 exited with status 1.
> > > PSIlogger: Child with rank 5 exited with status 1.
> > > forrtl: error (78): process killed (SIGTERM)
> > > PSIlogger: Child with rank 0 exited with status 1.
> > > PSIlogger: Child with rank 4 exited with status 1.
> > > forrtl: error (78): process killed (SIGTERM)
> > > forrtl: error (78): process killed (SIGTERM)
> > > PSIlogger: Child with rank 2 exited with status 1.
> > >
> > > please help.
> > >
> > > Regards
> > > ------------------------------
> > > Here's a new way to find what you're looking for - Yahoo! Answers
> > > <http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>
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> >
> >
> >
> >
> > ------------------------------
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>
>
>
>
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Received on Wed Jun 20 2007 - 06:07:23 PDT
