it won't make the rst until it ends, so as others have suggested
you need to find out why the job is stopping before done.
trying setting nstlim to 10 and see if that works, then you'll
know why no rst is made in your current run. then you just need to figure
out how to adjust the run time in your batch program.
On 9/25/07, Su Nwe <snwe001.gmail.com> wrote:
>
> Thank you Carlos.
> That capital letter O did get rid of the error message. But it still
> didn't create rst file :(
>
> On 9/25/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > my guess is that the -i is being interpreted as your output file
> > since it is right after -o, and then the min_kelly.in is what it thinks
> is
> > the next flag. You probably mean to say "sander -O" with a capital
> > letter O rather than lower case.
> >
> > On 9/25/07, Su Nwe <snwe001.gmail.com> wrote:
> > >
> > > Thanks you all for answering my questions.
> > >
> > >
> > > This is the code I typed in for minization:
> > > $AMBERHOME/exe/sander -o -i min_kelly.in -o min_kelly.out -p
> > > kelly.prmtop -c kelly.inpcrd -r min_kelly.rst
> > >
> > > I added igb=6 and ntb=0 to my input file. ... (Thanks to David C. and
> > > Carlos S :)
> > >
> > > This is the error message I got (printed to terminal):
> > > mdfil: Error unknown flag: min_kelly.in
> > >
> > > usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r
> restrt
> > > [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
> > > -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
> > > mdinfo -radii radii]
> > > Consult the manual for additional options.
> > >
> > > Mr. Walker: I do not understand what you mean by this.
> > > "How exactly are you running the minimizations - interactively or
> through
> > a
> > > queuing system?"
> > >
> > >
> > > And I forgot to mention this: I'm running Amber 9 on Mac OS X 10.4.10
> > >
> > > On 9/25/07, David A. Case <case.scripps.edu> wrote:
> > > > On Tue, Sep 25, 2007, Su Nwe wrote:
> > > > >
> > > > > I'm trying to run a simple molecular dynamic "without solvent" on
> an
> > > > > organic molecule using Amber 9. I could neither do minimization
> nor
> > > > > molecular dynamics. I'm assuming that I made some errors in
> setting
> > > > > parameters.
> > > > >
> > > > > The following is my minimization input file.
> > > > > initial minimisation
> > > > > &cntrl
> > > > > imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=0
> > > > > /
> > > >
> > > > The default in sander is ntb=1, that is, for a periodic box with
> > solvent.
> > > > If you want a simulation "without solvent", you need to specific
> ntb=0.
> > > >
> > > > >
> > > > > I tried running the system "with solvent". Both minimization and
> > > > > molecular dynamic works, but when I looked at the molecule (.mdcrd
> > > > > file) using VMD, the molecules were shooting out everywhere and
> moving
> > > > > so randomly.
> > > >
> > > > This sounds correct: if you want the animation to look "nice" (with
> all
> > the
> > > > molecules in the central unit cell,) you need to use the "image"
> command
> > in
> > > > ptraj to re-pack everything into the central unit cell.
> > > >
> > > > These may not be the only problems, but I hope they will get you
> going
> > in the
> > > > proper direction.
> > > >
> > > > ....dac
> > > >
> > > >
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> >
> >
> >
> >
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Received on Wed Sep 26 2007 - 06:07:26 PDT
