[gmx-users] problem with trjconv

[Mark Abraham]

nitu sharma wrote:
> Dear all
> 
>                      I am on the final step of  MD simulation of 
> membrane protein . the final mdrun has successfully  completed after 
> that I have filtered the water from the system .next step is to convert 
> it in final pdb to view it in pymol for this  I am using "trjconv" in 
> this step I have to  select a group from this option-
> 
> Group     0 (      System) has 419010 elements
> Group     1 (     Protein) has  9902 elements
> Group     2 (   Protein-H) has  7778 elements
> Group     3 (     C-alpha) has  1000 elements
> Group     4 (    Backbone) has  3000 elements
> Group     5 (   MainChain) has  4000 elements
> Group     6 (MainChain+Cb) has  4922 elements
> Group     7 ( MainChain+H) has  4961 elements
> Group     8 (   SideChain) has  4941 elements
> Group     9 ( SideChain-H) has  3778 elements
> Group    10 ( Prot-Masses) has  9902 elements
> Group    11 ( Non-Protein) has 409108 elements
> Group    12 (        DMPC) has  5520 elements
> Group    13 (         SOL) has 403578 elements
> Group    14 (         NA+) has    10 elements
> Group    15 (       Other) has 409108 elements
> Select a group:
> 
> for protein with lipid bilayer which group is suitable can anyone 
> suggest me?

It seems to me that you haven't actually "filtered water", but that you 
may wish to create a suitable index group. See 
http://oldwiki.gromacs.org/index.php/Index_File

Mark

> Becoz a/c to my opinion in group 0 there may be water also but I want to 
> remove water .
> so please if anyone have idea about this please suggest me .
> 
> thanks a lot.
> 
> Nitu Sharma.
> 
> 
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