[gmx-users] problem during energy minimisation to allow only hydrogen molecule to relax

[XAvier Periole]

you could use position restrains on the other atoms (non hydrogens) or  
use freezing groups.

it seems that your system has a major problem: bad contacts ... check  
it prior to EM.

On Jul 6, 2009, at 8:30 AM, nitu sharma wrote:

> Dear all
>
>
>   I have to apply only Hydrogen molecule will be relax during energy  
> minimization of protein molecule.
>
> can anyone have idea about what short of changes I have to make in  
> em.mdp file to allow only hydrogen molecule is relaxable during  
> energy minimisation?
> my em.mdp file like this-
>
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.001
> nsteps              =  100
>
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  10
> emstep              =  0.01
> nstcgsteep          =  1000
> nstcomm             =  1
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> vdw-type            = cut-off
> rvdw                =  1.0
> coulombtype         =  PME
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> comm-mode           = Linear
> pbc                 = XYZ
> Thanks a lot in advance.
>
> Nitu sharma.
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