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
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Received on Mon Jun 13 2011 - 08:00:03 PDT
