[gmx-users] Selecting two groups in trjconv

Irem Altan irem.altan at duke.edu
Tue Oct 20 17:20:23 CEST 2015


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,


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