Actually I suspect this is about SHAKE. It needs to make sure the heavy
atoms and the attached hydrogens are on the same processor.
I don't think this is a limitation in pmemd- you might try using that.
On Mon, Jun 13, 2011 at 10:36 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> I should caveat that I believe this limitation may actually only apply for
> NPT simulations. Hence you could in principal modify the code to skip the
> error message if you are NOT running NPT although you will of course need
> to
> test this.
>
> In reality though you can just break up your molecule into smaller
> residues.
> Ultimately just have 1 atom per residue. It is really just a setting up
> issue than a practical one.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Jason Swails [mailto:jason.swails.gmail.com]
> > Sent: Sunday, June 12, 2011 4:15 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] About "Must have more residues than processors"
> >
> > On Sun, Jun 12, 2011 at 2:35 PM, Bin Wu <wubin2002.gmail.com> wrote:
> >
> > > Dear Amber Users,
> > >
> > >
> > > I have a question about using parallel amber.
> > >
> > >
> > > I managed to configure and installed serial and parallel version of
> > amber
> > > on
> > > my desktop which has Ubuntu 64bit operating system. And it passed
> > almost
> > > all
> > > of the testing, for both serial and parallel.
> > >
> > > Now I intend to run simulation on my own polymer--- dendrimer, which
> > has a
> > > repeat unit. The PDB file is created using Material Studio. I
> > followed the
> > > steps described in the tutorial and the simulation on serial version
> > of
> > > sander worked just fine.
> > >
> > > Once I tried to go parallel, it gave me tons of troubles.
> > >
> > > When I intend to launch the simulation by "mpirun -np 2 sander.MPI -O
> > -i
> > > eq.in -o DenG3.out -p DenG3.prmtop -c DenG3.crd -r DenG3.rst -x
> > > DenG3.mdrcd
> > > &"
> > >
> > > It gives me an error saying "Must have more residues than
> > processors". So
> > > I looked into the prmtop file and learned it is true that there is
> > only one
> > > residue defined. And then I looked into the pdb file generated by
> > material
> > > studio, the "residue sequence number" is all set 0.
> > >
> >
> > This is true for sander. For pmemd, however, the restriction is simply
> > that
> > the number of atoms must be at least 10x the number of processors,
> > which is
> > an arbitrary limit loosely based on the idea that if you split the
> > workload
> > up any more, communication will limit your scaling (and probably make
> > it
> > even slower than running on fewer processors). sander has a more naive
> > approach to splitting the workload, and does so by residue (hence the
> > message you're seeing).
> >
> >
> > >
> > > So I figured it might be the problem. Then I manually change the
> > "residue
> > > sequence number" grouping each repeat unit to have the same "residue
> > > sequence number". Finally there are 61 residue. Based on my
> > understanding,
> > > it could ran on at least 60 processors.
> > >
> >
> > It *should* run on 61, but using that many processors is a poor idea,
> > in my
> > opinion (and most other peoples' opinions as well, I'm sure).
> >
> > >
> > > However, when I intend to use "antechamber" to prepare the mol2 file,
> > it
> > > gives me another error saying "Warning: detected more than 10 Residue
> > > sequence numbers:" and also "cannot run judgebontype() of
> > antechamber.c
> > > properly, exit".
> > >
> >
> > Antechamber is mainly useful for *single* residues. Thus, if your
> > system is
> > a truly repeating polymer, then you should be able to create a mol2
> > file for
> > just 1 monomer, and it will use that definition for every unit in your
> > system. Another useful utility for this is R.E.D. tools (
> > http://q4md-forcefieldtools.org/). See some of their tutorials for
> > details
> > on creating force field libraries.
> >
> >
> > >
> > > My questions is
> > >
> > > 1) Is it true that the number of residues must be greater than the
> > number
> > > of
> > > processors one wanted to use? So if I want to use 120 cores, do I
> > have to
> > > have at least 121 residues in my simulation system?
> > >
> >
> > No, at least 120 for sander, or 1200 atoms for pmemd. However,
> > actually
> > going out to this limit is not advisable. You'll be wasting resources.
> >
> >
> > >
> > > 2) If the answer to my first question is positive, why I could not
> > prepare
> > > mol2 file using antechamber for a system only have 61 residues?
> > >
> >
> > Antechamber isn't designed for a 60-residue system. See my comments
> > above.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Jun 13 2011 - 08:00:04 PDT
