[gmx-users] Energy from a subgroup of molecules
paul buscemi
pbuscemi at q.com
Fri Apr 12 15:35:17 CEST 2019
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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> Justin A. Lemkul, Ph.D.
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