[gmx-users] remove dummies how-to

Anton Feenstra feenstra at chem.vu.nl
Thu Jun 13 12:51:37 CEST 2002

Dmitry Kovalsky wrote:

> Hi there,
> I have simulated with dummies and now want to remove them and continue the 
> simulation. Is it possible  to remove dummies from system and preserve all 
> other environment so I will not have to create a box again, solvate my 
> protein etc?

Yes -- it involves a few steps:
1) create topology without dummies:
    re-run pdb2gmx but without -dummy option, then add the appropriate
    amount of Solvent (SOL) and possibly other molecules, identical to
    what you already have in your original (with dummies) topology.
2) create coordinates without dummies (for -NH3/-CH3 groups, some
    additional 'dummy-mass atoms' are created):
    using make_ndx, make an .ndx (index) file wihout the 'dummy-mass
    atoms' by the command '! a M*' (selects all atoms which names do
    not start with an 'M').
    using trjconv and the new .ndx file, convert the .trr file (full
    precision) to a version without the 'dummy-mass atoms'.
3) using grompp create a new .tpr file from this .top file.
    then, using tpbconv, create from the new .tpr and new .trr file
    an even newer .tpr file which has the 'new' topolgy (that we just
    created using pdb2gmx/grompp) but the 'old' coordinates and
    velocities (that we got from the old .trr using trjconv).

If you need to adjust parameters in the .mdp file, do that before
you run grompp. (some old versions of tpbconf read a .mdp file, but
that does not work)

Hope this helpes...



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