Re: [AMBER] problems ahout simulating a molecular crystal

From: hanlu0366 <hanlu0366.gmail.com>
Date: Fri, 10 Jun 2011 15:11:13 +0800

Dear sir :

The edition of Amber is Amber 11. The fllowing file is my inputfiles of minimization.
In the assesory ,the crd is supercell 5*10*4 which is sourced from pdb established by Propdb in AmberTools 1.5 . At same time , I change the parameters of box by ChBox in AmberTools 1.5. The parameters of Unitcell
a=10.906 b= 3.991 c= 14.030 alpha=90 Belta= 110.82 gamma=90 . The parameters of box is 58.0000000 45.0000000 60.0000000 90.0000000 110.8200000 90.0000000 . There are 5 monomers in Unitcell , each monomer contains 20 atoms.
1.index
 min.in

&cntrl
  imin = 1,
  maxcyc = 500,
  ncyc = 250,
  ntb = 1,
  igb = 0,
  ntr = 0,
  cut = 16
 /






  


2011-06-10



hanlu0366



发件人: David A. Case
发送时间: 2011-06-10 00:59:48
收件人: AMBER Mailing List
抄送:
主题: Re: [AMBER] problems ahout simulating a molecular crystal
 
On Thu, Jun 09, 2011, hanlu0366 wrote:
>
> I am trying to run a minimization of a solid organical molecuar crystal
> . In it ,each monomer embraces 20 atoms. The structure is Triclinic .
> I established a 5*10*4 supercell containing 20000 atoms. when excuting
> process of minimization,I
> came accross the fllowing error :
>
> * NB pairs 13761 38869173 exceeds capacity ( 38880000)
> SIZE OF NONBOND LIST = 38880000
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
We need more information. First, you are using an old version of sander, but
I'm unsure how old. But a 20000 atom system should not be giving this error.
What does your input file look like, and in particular, what value of "cut"
are you using?
....dac
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Received on Fri Jun 10 2011 - 00:30:03 PDT
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