[gmx-users] The energy output code

Shao Qing shaoqingfly1981 at gmail.com
Wed Jun 21 13:13:04 CEST 2006

Thanks Mark for your reply. I think I have not express myself clearly.  
 I do not plan to do this during the MD run but after the MD run. 
For example, I have two groups 
A 1 2 3 4 
B 5 6 7 8
I want to calculate the enery between group A and group B, but need some additive criterion to make sure, say, the interaction enery between 1 and 5 should be added to the sum or not. 
I wish to find the energy code of the gmx to output edr, then maybe I can modified it.
I still cannot find the src code of the subroutine.
Or any other good method?
>>Shao  Qing  wrote:
>> Gromacsers:  
>>  Hello,  everyone.  I  want  to  calculate  the  interaction  energy  of  molecules  in  certain  region,  like  in  the  pore.  Because  the  molecules  can  move  inside  the  pore  and  outside  it.  A  group  is  not  suitable  here,  I  guess.  I  do  not  find  such  tools  in  the  gmx_tools,  either.  I  want  to  change  the  code  of  the  subroutine  output  energy  in  the  mdrun  to  fulfill  my  aim.  Could  anyone  tell  me  where  the  subroutine  is?  I  mean,  the  subroutine  to  calculate  the  energy  in  the  mdrun  and  output  it  to  the  edr.
>> Thanks  in  advance    
Mark wrote
> Caveat,  I'm  not  expert  enough  to  be  sure  what  I'm  saying  is  right,  but  I
think  it  right!

> It's  not  as  simple  as  that.  The  energies  (and  forces)  are  computed
group-wise,  so  you  need  to  construct  a  group  back  in  the  .top  file
before  evaluating  the  energy.  The  simplest  way  to  do  that  would  be  to
decided  in  advance  how  many  water  molecules  will  be  in  the  group,  and  at
each  energy  output  step,  recompute  exactly  which  water  molecules  are
close  enough  to  be  part  of  the  group,  and  fill  the  group  data  structure
with  the  corresponding  indices.  Then  magically  the  energy  for  that  group
will  be  calculated  and  appear  in  the  .edr  output.

> Mark


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