AMBER Archive (2008)
Subject: Re: AMBER: Non bond list error

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Oct 24 2008 - 11:40:24 CDT

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Have you built pmemd? It is a separate step after the general build of amber. If you have built it, is it somewhere that it can be found? Here you just reference it as "pmemd" with no path. I generally use something like $AMBERHOME/exe/pmemd, ASSUMING it has been built...
Regards - Bob Duke
  ----- Original Message -----
  From: neville forlemu
  To: amber_at_scripps.edu
  Sent: Friday, October 24, 2008 12:34 PM
  Subject: RE: AMBER: Non bond list error

Hi Ross,

I did change the parameters you suggested to their defaults, and also changed the forcefield type, but got the same error from sanders.

        However when I try pmemd this is the error I got
        mpirun -np 4 pmemd -O -i minwat.in -o minwat.out -p rldhn_sol.top -crldhn_sol.crd -r minwat.resrst -ref rldhn_sol.crd
        MPI: brinsvr1: 0x6c6bffff00005964: /usr/local/gnu/bin/bash: line 1: exec: pmemd: not found
        MPI: could not run executable (all_signal.c:206)

Neville

--- On Fri, 10/24/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

          From: Ross Walker <ross_at_rosswalker.co.uk>
          Subject: RE: AMBER: Non bond list error
          To: amber_at_scripps.edu
          Date: Friday, October 24, 2008, 1:12 AM

Hi Neville

You have a valid reason for this:

scnb = 1.0, scee = 1.0, ??????

You should NEVER EVER mess with the defaults of these values unless you know exactly what you are doing, i.e. using a non standard force field that uses different 1-4 scaling factors. Setting these to 1.0 for the AMBER FF series force fields will invalidate ALL of your results.

Note you also probably do not want to be using FF99. I suggest using FF99SB or FF03.

You should also not be messing with nsnb - leave that at the default as well.

As for the Non bond list overflow problem try setting cut=8.0 and see if it goes away.

All the best

Ross

          From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of neville forlemu
          Sent: Thursday, October 23, 2008 10:13 PM
          To: amber_at_scripps.edu
          Subject: RE: AMBER: Non bond list error

Hi Ross

I am using amber8 and trying to use sanders to minimize waters around this huge protein of about 20000 atoms, then perform a short md on some residues in the protein.

                Constant Volume Minimization
                 # Control section
                 &cntrl
                  ntwx = 500, ntpr = 500, ntwr = 500,
                  scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 12.0,
                  ntb = 1, ntc = 2, ntf = 2,
                  maxcyc = 10000, ntmin = 1, ncyc = 1000, drms = 0.0001,
                  ntp = 0,
                  ibelly = 0, ntr = 1,
                  imin = 1,
                 &end
                Group Input for restrained atoms
                5.0
                RES 1 1332
                END
                END

Thanks

                Neville
                Also below is the xleap file preparation
                Welcome to LEaP!
                (no leaprc in search path)
> source leaprc.ff99
                ----- Source: /opt/brinsoft/amber8/dat/leap/cmd/leaprc.ff99
                ----- Source of /opt/brinsoft/amber8/dat/leap/cmd/leaprc.ff99 done
                Log file: ./leap.log
                Loading parameters: /opt/brinsoft/amber8/dat/leap/parm/parm99.dat
                Loading library: /opt/brinsoft/amber8/dat/leap/lib/all_nucleic94.lib
                Loading library: /opt/brinsoft/amber8/dat/leap/lib/all_amino94.lib
                Loading library: /opt/brinsoft/amber8/dat/leap/lib/all_aminoct94.lib
                Loading library: /opt/brinsoft/amber8/dat/leap/lib/all_aminont94.lib
                Loading library: /opt/brinsoft/amber8/dat/leap/lib/ions94.lib
                Loading library: /opt/brinsoft/amber8/dat/leap/lib/solvents.lib
> x = loadpdb rldhN.pdb
                Loading PDB file: ./rldhN.pdb
                 (starting new molecule for chain B)
                 (starting new molecule for chain C)
                 (starting new molecule for chain D)
                  total atoms in file: 10236
                  Leap added 10556 missing atoms according to residue templates:
                       10556 H / lone pairs
> savepdb x rld.pdb
                Writing pdb file: rld.pdb
                 Shortening residue name for PDB format: NALA -> ALA
                 Shortening residue name for PDB format: CPHE -> PHE
                 Shortening residue name for PDB format: NALA -> ALA
                 Shortening residue name for PDB format: CPHE -> PHE
                 Shortening residue name for PDB format: NALA -> ALA
                 Shortening residue name for PDB format: CPHE -> PHE
                 Shortening residue name for PDB format: NALA -> ALA
                 Shortening residue name for PDB format: CPHE -> PHE
> y = loadpdb rld.pdb
                Loading PDB file: ./rld.pdb
                  total atoms in file: 20792
> addions y Cl- 0
                8 Cl- ions required to neutralize.
                Adding 8 counter ions to "y" using 1A grid
                Grid extends from solute vdw + 2.47 to 8.47
                Resolution: 1.00 Angstrom.
                grid build: 1 sec
                 (no solvent present)
                Calculating grid charges
                charges: 251 sec
                Placed Cl- in y at (5.12, -4.35, -51.18).
                Placed Cl- in y at (4.12, 4.65, 0.82).
                Placed Cl- in y at (13.12, -39.35, -35.18).
                Placed Cl- in y at (-3.88, 16.65, -2.18).
                Placed Cl- in y at (29.12, -0.35, -20.18).
                Placed Cl- in y at (-8.88, -29.35, 3.82).
                Placed Cl- in y at (-9.88, 32.65, -53.18).
                Placed Cl- in y at (-27.88, -7.35, -31.18).

                Done adding ions.
> solvateBox y TIP3PBOX 10
                  Solute vdw bounding box: 76.168 91.281 70.396
                  Total bounding box for atom centers: 96.168 111.281 90.396
                  Solvent unit box: 18.774 18.774 18.774
                  Total vdw box size: 99.135 92.364 120.398 angstroms.
                  Volume: 1102429.931 A^3
                  Total mass 702324.416 amu, Density 1.058 g/cc
> saveamberparm y rldhn_sol.top rldhn_sol.crd
                Checking Unit.
                Building topology.
                Building atom parameters.
                Building bond parameters.
                Building angle parameters.
                Building proper torsion parameters.
                Building improper torsion parameters.
                 total 3824 improper torsions applied
                Building H-Bond parameters.
                Not Marking per-residue atom chain types.
                Marking per-residue atom chain types.
                  (Residues lacking connect0/connect1 -
                   these don't have chain types marked:

--- On Thu, 10/23/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

                From: Ross Walker <ross_at_rosswalker.co.uk>
                Subject: RE: AMBER: Non bond list error
                To: amber_at_scripps.edu
                Date: Thursday, October 23, 2008, 11:56 PM

Hi Neville,

Can you post your input file and some details about your system (number of atoms, type of simulation, gas phase, periodic boundaries etc) as well as the version of AMBER you are using.

All the best

Ross

                From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of neville forlemu
                Sent: Thursday, October 23, 2008 9:48 PM
                To: amber_at_scripps.edu; rduke_at_email.unc.edu
                Subject: Re: AMBER: Non bond list error

Hello,

Could some one explain to me what this error means

                       * NB pairs 7104 103754005 exceeds capacity ( 103754298) 0
                           SIZE OF NONBOND LIST = 103754298
                       SANDER BOMB in subroutine nonbond_list
                       Non bond list overflow!
                       check MAXPR in locmem.f

I am trying to run sander for energy minimization, but keep running into this problem.

Thanks

--- On Thu, 10/23/08, Robert Duke <rduke_at_email.unc.edu> wrote:

                      From: Robert Duke <rduke_at_email.unc.edu>
                      Subject: Re: AMBER: Non bond list error
                      To: amber_at_scripps.edu
                      Date: Thursday, October 23, 2008, 3:44 PM

Actually, I noticed I said "you overflowed the counter", and then show

    that

    you didn't... (oh, oops). So it is memory corruption. What I don't

    understand is why you are not dying with some sort of "out of memory"

    error

    from sander, associated with asking for more memory than is available. For

    pmemd, anywhere I allocate dynamic memory, I check for a success return

    code, so the way you should experience running out of memory there is to get

    an explicit error message. Because sander has a preallocated memory pool

    strategy, I suspect that other things are possible... Bottom line on all

    this - I think it is a good idea to not run more than roughly 100,000 atoms

    on a single processor, especially for sander. And if you run it on 4

    processors but they all share the same limited physical memory, you may also

    hit trouble. I attached a graphic on pmemd memory requirements - a jpg so

    it should be widely viewable. My rule of thumb for pmemd is that 4

    processors, each with 1 GB of actual physical memory, can handle up to 1

    million atoms with the default 8 angstrom cutoff. Sander will take more.

    There are also buffer space considerations in an mpi application (within mpi

    itself, not in the app), that further muddy the waters, but following this

    guideline you should be safe.

    Regards - Bob



    ----- Original Message -----

    From: "Robert Duke" <rduke_at_email.unc.edu>

    To: <amber_at_scripps.edu>

    Sent: Thursday, October 23, 2008 4:14 PM

    Subject: Re: AMBER: Non bond list error





> As Ross will tell you too:

> 1) Don't increase cut to 12, leave it at the default (of 8)

> 2) Run this on at least 4 processors using the MPI version of pmemd or

> sander (I know you are using sander here; pmemd requires less memory).

> Even higher processor counts will reduce your risk of memory overflow

> further. Your pairlist went negative because you incremented it past a 31

> bit digit; with the commonly used integer format on computers these days

> (twos-complement), this results in a negative number (and is clearly an

> error condition). Is this memory usage reasonable for the size problem

> you have? Well, that cutoff plus skin will produce about 552 pairs per

> atom. If you had 1,000,000 atoms (and you are close), that would be

> 552,000,000 pairs. Not enough to overflow the list counter. BUT that is

> 552,000,000 pairs * 4 bytes per integer, means 2 GB in the nonbonded list

> alone. Most machines, you are pushing it to get much over 1.5 GB for the

> application (I have not looked recently, so that is off the top of my

> head). With true 32 bit executables, you are out of address space; with

> the newer 64 bit chips, you have bits to specify more than 2 GB of

> addresses, but you may not have enough actual memory. And remember that

> the pairlist is only part of your memory consumption. No resource is

> infinite on a computer...

> Regards - Bob Duke

> ----- Original Message -----

> From: "Wang,Ying" <wangying_at_ufl.edu>

> To: <amber_at_scripps.edu>

> Sent: Thursday, October 23, 2008 3:26 PM

> Subject: RE: AMBER: Non bond list error

>

>

>> Hi, Ross,

>>

>> Thanks a lot!

>>

>> My input file is as below:

>> 50ps MD with res

>> &cntrl

>> imin = 0,

>> irest = 0,

>> ntx = 1,

>> ntb = 1,

>> cut = 12,

>> ntr = 1,

>> ntc = 2,

>> ntf = 2,

>> tempi = 0.0,

>> temp0 = 300.0,

>> ntt = 3,

>> gamma_ln = 2.0,

>> nstlim = 50000, dt = 0.001

>> ntpr = 1000, ntwx = 1000, ntwr = 1000

>> nmropt=1

>> /

>> &wt TYPE='TEMP0', istep1=0, istep2=50000,

>> value1=0.1, value2=300.0, /

>> &wt TYPE='END' /

>> Keep system fixed with weak restraints

>> 20.0

>> RES 1 5076

>> END

>> END

>>

>> and the NPT is as below:

>>

>> NPT: 50ps MD

>> &cntrl

>> imin = 0, irest = 1, ntx = 7,

>> ntb = 2, pres0 = 1.0, ntp = 1,

>> taup = 2.0,

>> cut = 12, ntr = 1,

>> ntc = 2, ntf = 2,

>> tempi = 300.0, temp0 = 300.0,

>> ntt = 3, gamma_ln = 2.0,

>> nstlim = 50000, dt = 0.001,

>> ntpr = 1000, ntwx = 1000, ntwr = 1000

>> /

>> Keep fixed with weak restraints

>> 20.0

>> RES 217 954

>> END

>> Keep fixed with weak restraints

>> 20.0

>> RES 1909 2646

>> END

>> Keep fixed with weak restraints

>> 20.0

>> RES 3601 4338

>> END

>> res also

>> 5.0

>> RES 955 1692

>> END

>> res also

>> 5.0

>> RES 2647 3384

>> END

>> res also

>> 5.0

>> RES 4339 5076

>> END

>> END

>>

>>

>>

>> Thanks again!!!!!!!!!!!!!!!

>>

>>

>>

>> On Thu Oct 23 14:38:09 EDT 2008, Ross Walker

    <ross_at_rosswalker.co.uk>

>> wrote:

>>

>>> Hi Wang,

>>>

>>> 800K atoms is pretty large and while sander / pmemd should support

    this

>>> size

>>> (I think 999,999 is the limit right now due to file formatting)

    you may

>>> run

>>> into problems that haven't been seen before.

>>>

>>> It's not obvious what is going wrong in your case but the

    numbers don't

>>> make

>>> any sense (a negative capacity!) which suggests either memory

    corruption

>>> through an array overflow or the number of pairs is larger than a

    signed

>>> integer and is overflowing. Even at 800K atoms you shouldn't

    have this

>>> many

>>> pairs though. Can you post your input file so we can take a look?

    I

>>> suspect

>>> you have cut set too high or perhaps are not running PME etc.

>>>

>>> All the best

>>> Ross

>>>

>>>> -----Original Message-----

>>>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]

    On

>>>> Behalf

>>>> Of Wang,Ying

>>>> Sent: Thursday, October 23, 2008 10:20 AM

>>>> To: amber_at_scripps.edu

>>>> Subject: AMBER: Non bond list error

>>>>

>>>> Hi, Dear AMBERs,

>>>>

>>>> I meet a problem when I run a simulation of a system consist

    of

>>>> 799889 atoms.

>>>>

>>>> * NB pairs 451 0 exceeds capacity (

>>>> -28510921) 7

>>>> SIZE OF NONBOND LIST = -28510921

>>>> SANDER BOMB in subroutine nonbond_list

>>>> Non bond list overflow!

>>>> check MAXPR in locmem.f

>>>>

>>>> Could anyone tell me what's happen?

>>>>

>>>> Thanks a lot!

>>>>

>>>>

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>>>

>>>

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>>>

>>

>>

>>

>> --

>> Wang,Ying

>>

>>

    -----------------------------------------------------------------------

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--- On Thu, 10/23/08, Robert Duke <rduke_at_email.unc.edu> wrote:

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AMBER Archive (2008)Subject: Re: AMBER: Non bond list error

AMBER Archive (2008)
Subject: Re: AMBER: Non bond list error