[gmx-users] Selecting two groups in trjconv

[Deva Priya]

You can make an index file after the simulation.

Supply your index file with the option -n index.ndx to trjconv

The manual has an example of selecting Oxygen atoms

typically you can simply use a OW to select all atoms of name OW (which
would be oxygen of water) and to pick all HW1 and HW2 you use a HW*

Good luck,


On Tue, Oct 20, 2015 at 10:26 AM, Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
>
> I'm new to GROMACS, so forgive me if this question is too trivial. I am
> using version 4.6.5.
>
> I ran an MD simulation of a protein solvated in water in its unit cell. I
> have two kinds of water molecules, HO4 the crystal waters already available
> in the .pdb file, and SOL, the water molecules that I added into the unit
> cell. Both are modeled by tip4p. I would like to generate a .pdb file from
> the MD snapshots, including both HO4 and SOL.
>
>
> When I do trjconv -f nvt.trr -s nvt.tpr -b 0 -e 5001 -ur tric -pbc atom -o
> conf.pdb , I am given the following list of groups to choose from:
>
>
> Select group for output
> Group     0 (         System) has 11556 elements
> Group     1 (        Protein) has  4988 elements
> Group     2 (      Protein-H) has  2471 elements
> Group     3 (        C-alpha) has   314 elements
> Group     4 (       Backbone) has   942 elements
> Group     5 (      MainChain) has  1258 elements
> Group     6 (   MainChain+Cb) has  1560 elements
> Group     7 (    MainChain+H) has  1551 elements
> Group     8 (      SideChain) has  3437 elements
> Group     9 (    SideChain-H) has  1213 elements
> Group    10 (    Prot-Masses) has  4988 elements
> Group    11 (    non-Protein) has  6568 elements
> Group    12 (          Other) has  1660 elements
> Group    13 (            HO4) has  1660 elements
> Group    14 (             NA) has     6 elements
> Group    15 (             CL) has    14 elements
> Group    16 (            Ion) has    20 elements
> Group    17 (            HO4) has  1660 elements
> Group    18 (             NA) has     6 elements
> Group    19 (             CL) has    14 elements
> Group    20 (          Water) has  4888 elements
> Group    21 (            SOL) has  4888 elements
> Group    22 (      non-Water) has  6668 elements
> Group    23 ( Water_and_ions) has  4908 elements
>
>
> I would like to be able to select both HO4 and SOL. Moreover, I would like
> to be able to select only OW atoms of both groups (currently they contain
> OW, HW1, HW2, and MW). Now, I understand that I have to create an .ndx file
> to group what I want together. One question is, can I create the .ndx file
> at this stage (after having run the simulation) and feed it into trjconv?
> My second problem is, I am really confused about how make_ndx works. Could
> you guide me through it or point me to a comprehensive guide or tutorial?
>
>
> Thank you,
>
> Irem
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