[gmx-users] how to build the input files of an infinite system

[silvester.thu]

Thanks, Mark

I am so sorry about my failure to describe my problem clearly. My problem is that while I was doing EM with that infinite system, the Fmax was unreasonably large (~1e4). But just now, I changed the pbc=xyz to pbc=full in my em.mdp file, then it is OK now. 
So I have a new question now: as the pbc=full has never been mentioned in GROMACS 3.3 manual, what is the difference between pbc=full and pbc=xyz?

I have checked the example of CNT on the website you mentioned. I do not use x2top in my simulation, because I generate the input .gro and .itp files directly with other programs. I manually add the topology among atoms on the neighboring edges of graphene and its image. But the pbc=full mentioned in that example is very helpful. 

Thanks for your suggestion!




silvester.thu
2008-05-15



发件人： Mark Abraham
发送时间： 2008-05-15 10:29:49
收件人： Discussion list for GROMACS users
抄送： 
主题： Re: [gmx-users] how to build the input files of an infinite system

silvester.thu  wrote:
>  Hello  everyone,
>    
>  I  am  working  on  a  simulation  of  an  infinite  system  but  I  do  not  know  how  
>  to  build  its  periodic  boundary  conditions  in  GROMACS.  My  system  is  a  
>  graphene  that  is  infinite  on  a  certain  direction.  Surely  I  can  not  
>  generate  an  infinitely  large  graphene  for  input.  So  I  want  to  make  a  
>  finite  graphene  to  repeat  along  a  certain  direction  in  order  to  
>  approximate  the  "infinite"  one  (e.g:  spread  the  finite  graphene  from  
>  left  to  right).  But  I  do  not  know  the  technical  details.  Anyone  have  
>  experience  on  this  kind  of  problems?

Yes.  You  can  probably  adapt  the  advice  here
http://wiki.gromacs.org/index.php/Carbon_Nanotube  to  your  needs.

>  I  have  tried  to  use  the  PBC  in  GROMACS,  and  add  the  bonds,  angles  and  
>  dihedrals  between  atoms  on  the  left  edge  and  atoms  on  the  right  edge  and  
>  make  the  size  of  box  to  be  just  the  same  as  the  sum  of  length  of  C-C  
>  bond  and  the  width(the  distance  from  the  left  edge  to  the  right  edge)  of  
>  graphene.  But  it  did  not  work.
>    
>  Anyone  can  give  me  some  advice?  It  will  be  very  helpful.

Describing  failure  with  "It  did  not  work"  makes  it  impossible  for  us  to
give  free  advice  at  a  rate  that  is  worth  our  time.  A  detailed
description  of  what  you  did  and  what  happened  is  almost  always  much  more
valuable  and  a  better  use  of  everybody's  time  than  the  alternative  :-)
See  the  advice  here  http://wiki.gromacs.org/index.php/Support

Mark
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