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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.
Please do not use, copy or disclose the information contained in this
message or in any attachment. Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.
This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 24 2015 - 09:30:03 PDT
