[gmx-users] Energy from a subgroup of molecules

[paul buscemi]

Thank you Justin.  

Using energy groups is not really that bad.  

By using  gmx select ‘atomname Cx and resname ADSORBATE and within 0.5 of resname SURFACE’ -on near.ndx

I can find  the atom/s of the adsorbate that is proximal to the surface and  can track the LJ pot’l by frame and use VMD for further analysis

Paul

> On Apr 11, 2019, at 5:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 4/11/19 5:39 PM, paul buscemi wrote:
>> Thank you for the response, Mark.
>> 
>> I do use the rerun tactic, and this is not too bad for a small number of molecules
>> 
>>  but is there a way to include the index information within the mdrun (rerun ) … something like
>> 
>> gmx mdrun  -s adsorb.ener_gp.tpr  -rerun adsorb,npt.trr   - n use_only.ndx  ?
>> 
>> or use the  indices within the grompp command ?
>> 
> 
> The only solution is what Mark proposed - create a .tpr file with the required energygrps and use mdrun -rerun. mdrun does not accept an index file.
> 
> -Justin
> 
>> Paul
>> 
>>> On Apr 11, 2019, at 1:48 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> You can't do that with gmx energy, as you need mdrun to understand the new
>>> grouping. But making a new .tpr with the energy groups so defined permits
>>> you to use gmx mdrun -rerun for such a single point energy evaluation.
>>> 
>>> Mark
>>> 
>>> On Wed., 10 Apr. 2019, 22:24 p buscemi, <pbuscemi at q.com> wrote:
>>> 
>>>> Dear Users,
>>>> I've performed an adsorption experiment in which a fraction of molecules
>>>> in solution adsorb to a surface. I can extract the index of those adsorbed,
>>>> and I can obtain the total interaction ( LJ ) of the energy group with the
>>>> surface.
>>>> I can estimate the average interaction of the adsorbed molecules by
>>>> dividing the total energy by the number of molecules within a certain
>>>> distance ( the index number )
>>>> How might I use gmx energy to recalculate the interaction using the
>>>> original surface but only the adsorbed molecules specified in the index
>>>> file... something like
>>>> "gmx energy -f starting.gro -n index.ndx"
>>>> 
>>>> A single point calculation would be quite satisfactory.
>>>> thanks
>>>> Paul
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