As I requested before, if you send me the prmtop file off-list, I will try
to determine what is happening.
At this stage, further guessing will likely be pointless.
All the best,
Jason
On Sun, Sep 27, 2015 at 1:23 PM, Damiano Spadoni <enxds6.nottingham.ac.uk>
wrote:
> #Dear Robert,
>
> thank you for your suggestion, but unfortunately this did not solve my
> problem. I changed my input file like the one below:
>
> 10ns MD with distance restraints on Fe4S4 - CYS
> &cntrl
> imin=0, irest = 1, ntx = 7,
> ntb=2, pres0 = 1.0, ntp = 1,
> taup=2.0,
> no_intermolecular_bonds = 0,
> cut=10.0, ntr = 1,
> ntc=2,
> ntf=2,
> tempi=300.0, temp0=300.0,
> ntt=3, ig=-1, gamma_ln=1.0,
> nstlim = 5000000, dt = 0.002,
> ioutfm=1, iwrap=1,
> ntpr=500, ntwx=500, ntwr=1000
> ntr=1,
> restraint_wt = 1.0,
> restraintmask = ':1639, 1642, 1645, 1648',
> /
> &wt
> type = 'DUMPFREQ',istep1=50
> /
> &wt type='END' /
>
> But even if I set no_intermolecular_bonds = 0, the error reply in the
> output files is the same:
>
> PMEMD does not support intermolecular PRFs!
>
> This thing is driving me mad, do you have any other ideas of what might be
> the cause of this??!
>
> Thanks,
> Damiano
>
> ________________________________________
> From: Duke, Robert E Jr [rduke.email.unc.edu]
> Sent: 24 September 2015 17:12
> To: AMBER Mailing List
> Subject: Re: [AMBER] hpc error
>
> Hi Diamiano,
>
> Okay, I am not "on top of" the current state of the Amber 14 source code,
> since I have been working on other force fields, BUT I am the guy that
> originally did pmemd, and the message you are seeing, at least in the Amber
> 10-12 timeframe, was generated when one is using extra points and there is
> an extra points frame (PRF) that spans across two prmtop molecule
> definitions (and I ported extra points to pmemd and parallelized the code
> after Darden put did a uniprocessor version in sander). The "fix" in
> pmemd,
> in that timeframe, was to introduce an algorithm that effectively redefined
> any covalently-bonded molecules as one molecule. This was the default
> behaviour in pmemd, which made it slightly different than the default
> behaviour in sander in terms of NTP ensembles, but the difference was
> really
> really minor, and I don't think either method is really superior. Anyway,
> one would only hit this if you had the molecule-spanning condition, AND you
> had set a &cntrl namelist variable in pmemd (no_intermolecular_bonds) to 0
> (it is or was, by default, 1), and you are using extra points. So check to
> be sure that no_intermolecular_bonds is 1.
>
> Apologies if I am "off course" on this - I just keyed on the error message,
> and looked back a couple of messages in the thread. I would expect this to
> only be happening if you are using extra points. It is entirely possible
> there is new stuff in Amber 14 I don't know about that impacts all this.
>
> Regards - Bob Duke
>
>
> ________________________________________
> From: Damiano Spadoni [enxds6.nottingham.ac.uk]
> Sent: Thursday, September 24, 2015 3:55 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] hpc error
>
> Dear Ambers,
>
> try running enzymes simulations an hpc ARCHER, I often receive the same
> error text whatever I change in my input file:
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
> As you suggested, I checked my topology file with checkValidity (this kind
> of errors may due to something wrong in the .prmtop file) and it detected
> two CYS residues being within 3A distance and it suggested to change the
> name of the residues and build a disulfide bond, without specifying which
> cysteines it is referring about.
> But the only cysteines that might be so close, are actually involved in
> binding a 4Fe-4S cluster (already double checked on VMD).
>
> So the questions are:
> - might it be a bug justifying its panicking error texts?
> - how to manually edit such residues to avoid this close contact (if you
> suggest so)?
>
> Many thanks
> Damiano
>
> ________________________________________
> From: David A Case [david.case.rutgers.edu]
> Sent: 18 August 2015 15:12
> To: AMBER Mailing List
> Subject: Re: [AMBER] hpc error
>
> On Tue, Aug 18, 2015, Damiano Spadoni wrote:
> >
> > I am trying to run the following script, involving a production step of
> > my simulation, on an hpc facility:
> >
> > #!/bin/bash --login
> >
> > #PBS -N S4F4_md
> > #PBS -l walltime=24:00:00
> > #PBS -l select=4
> > #PBS -j oe
> > #PBS -A e280-Croft
> >
> > module load amber
> >
> > cd /work/e280/e280/enxds6/SF4
> >
> > aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md1.out -p SF4.prmtop -c
> > S4F4_heat.rst -r S4F4_md1.rst -x S4F4_md1.mdcrd
> > aprun -n 96 sander.MPI -O -i S4F4_md.in -o S4F4_md2.out -p SF4.prmtop -c
> > S4F4_md1.rst -r S4F4_md2.rst -x S4F4_md2.mdcrd
> ....
>
> Oh my goodness....
>
> (1) When things are not working, start simple (a single sander run, not 6
> of then in sequence).
> (2) sander will almost certainly perform very badly (if at all)
> on 96 processors. Try running on 2 or 4 to start. Then you can test the
> timing of larger numbers.
>
>
> > partition error in shake on processor 2
> > this processor has atoms 13055 through 19568
> > atom 19568 is within this range
> > atom 19569 is not within this range !
>
> You should look at the output file from the part of the run that failed.
> Is it really running on 96 processors? How many atoms are in your system?
> (Message above suggests that you have some 13000 atoms per processor....)
> If you have a million atoms or more, try running your script a much smaller
> system, then gradually build up. Consider whether or not you can use pmemd
> instead of sander.
>
> > It is the first time I am trying tu run this simulation on a cluster, I
> > previously ran (just the first sander.MPI command) it on my machine and
> > it worked, but I want to repeat this simulation on a cluster.
> > Any suggestions about something I'm probably missing?
>
> Was your local run also with the same number of processors? The "partition
> error" means that the system is trying to SHAKE (constrain) the bond
> between
> atoms 19568 and 19569. Check these atoms: is atom 19569 a hydrogen that is
> bonded to atom 19568? Are those two atoms in different residues?
>
> It is possible that partition errors can arise, depending on how complex
> your
> system is. Since this depends on the number of processors you are using,
> it
> could well show up on a cluster but not on a "local machine" (which, I'm
> guessing, has fewer than 96 cores.)
>
> Using the "checkValidity" command in parmed may help you localize the
> problem.
>
> ...good luck...dac
>
>
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>
>
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> This message and any attachment are intended solely for the addressee
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> Please do not use, copy or disclose the information contained in this
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Sep 27 2015 - 13:00:03 PDT
