Hi Rejwan,
I suspect that something is wrong with your initial structure then -
perhaps the density is way too high, or the box size is completely wrong.
Something is leading to you having a VERY large pair list - I would
suspect the density is crazy high. How did you build your structure? -
Have you visualized it and checked it looks ok? Looked at it in VMD? Check
the bond lengths etc?
Try running it in serial first using just pmemd. It is possible the
installation of AMBER 12 on Stampede was not done right and or tested.
Also note you are asking for a VERY large number of cores:
#$ -pe 2way 180
There is little to no chance this will run efficiently with sander,
probably not with pmemd either - I'm not surprised sander just barfs, it's
unlikely to have been tested with more than 64 cores at most. PMEMD should
be fine at such a core count although I doubt you'll get very good
performance - especially for minimization which is far from optimized in
parallel.
Where did you come up with this core count from?
All the best
Ross
On 8/19/13 1:00 PM, "Rejwan" <rejwan_88.yahoo.com> wrote:
>Hi,
>
>I am trying to simulate a GPCR in POPC bi-layer. The minimization
>protocol is mainly based on following lipid tutorial link.
>
>http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Fiel
>d_Tutorial.html
>
>
>Minimize the lipid structure
> &cntrl
> imin=1,
> maxcyc=10000,
> ncyc=5000,
> ntb=1,
> ntp=0,
> ntf=1,
> ntc=1,
> cut=10.0,
> ntpr=50,
> ntwr=2000,
> &end
>/
>
>I'll update you on PMEMD run. However is there way to reduce/ignore
>non-bonded terms ? Thanks.
>
>Rejwan
>
>
>________________________________
> From: David A Case <case.biomaps.rutgers.edu>
>To: Rejwan <rejwan_88.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>Sent: Monday, August 19, 2013 3:31 PM
>Subject: Re: [AMBER] AMBER minimization job
>
>
>On Mon, Aug 19, 2013, Rejwan wrote:
>>
>> An AMBER minimization job was aborted due to overflow of non-bonded
>> list. My system is of 52 K atoms size. How I can perform minimization
>> in such situation ? Thank you.
>>
>>
>> Exit code -5 signaled from c321-214
>> * NB pairs 522 1219601 exceeds capacity ( 1219712) 23
>> SIZE OF NONBOND LIST = 1219712
>
>Can you post your min_lipid.in file? Also, try a short serial
>(non-parallel)
>run to see if the problem is specific to the parallel code. Trying pmemd
>instead of sander is also worth trying, since the nonbond lists are
>handled
>in a different way there.
>
>....dac
>
>
>_______________________________________________
>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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 19 2013 - 13:30:04 PDT
