AMBER Archive (2008)

Subject: RE: AMBER: Non bond list error

From: Wang,Ying (wangying_at_ufl.edu)
Date: Thu Oct 23 2008 - 14:26:26 CDT

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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> 

--
Wang,Ying

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