[gmx-users] Adsorption energy of a single molecule

[Darrell Koskinen]

Hi Justin,
In my simulation, I have just over 100 ammonia molecules and, of these 
molecules, 10 to 20 adsorb onto the graphene sheet.  I initially thought 
that I would need to tag each one of the ammonia molecules, since I 
would not know, in advance of running the simulation, which of these 
molecules would adsorb.

Are you suggesting that, after the initial simulation run, which uses an 
index file "index.ndx" and is comprised of three components {System, 
Grph, NH3}, I run make_ndx again to assign each adsorbed molecule to its 
own index, execute "mdrun -rerun mdtraj.trr -s mdtopol.tpr", where 
mdtraj.trr and mdtopol.tpr are the output of the initial simulation, and 
then use g_energy to analyze the energies between the groups?

Thanks.

Darrell
> Date: Sun, 01 Nov 2009 07:17:24 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Adsorption energy of a single molecule
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AED7C54.2080309 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Darrell Koskinen wrote:
>   
>> Hi Justin,
>> Thanks for the suggestion. I looked through the GROMACS manual and the 
>> only method I can see of obtaining the adsorption energy between an 
>> adsorbed ammonia molecule and the graphene sheet would be to create an 
>> index file that assigns a separate index for each ammonia molecule, run 
>> the simulation, and then run "gmxdump -e mdener.edr" to view the energy 
>> between the adsorbed ammonia molecule and the graphene sheet. Is this 
>> the method you are suggesting or is there a different method of 
>> obtaining this information?
>>
>>     
>
>  From your original message, I got the impression that only a few of your 
> ammonia molecules were adsorbed.  In this case, a better approach might be to 
> identify the molecules that adsorbed in your original simulation, create groups 
> for those individually, the graphene sheet, and then the rest of your ammonia. 
> Then use mdrun -rerun with your new .tpr file, and g_energy (not gmxdump) to 
> analyze the energies between the various groups.
>
> -Justin
>
>   
>> Thanks.
>>
>> Darrell
>>     
>>> Date: Thu, 29 Oct 2009 14:06:27 -0400
>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> Subject: Re: [gmx-users] Adsorption energy of a single molecule
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <4AE9D9A3.9080004 at vt.edu>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>
>>>
>>>
>>> darrellk at ece.ubc.ca wrote:
>>>  
>>>       
>>>> Dear GROMACS Gurus,
>>>> Is it possible to determine the adsorption energy of a single 
>>>> molecule in
>>>> a simulation? My simulation has a large number of gas phase molecules
>>>> distributed throughout a box with some molecules adsorbed on a graphene
>>>> sheet. I would like to compare the adsorption energy of a single
>>>> molecule to that reported in research papers.
>>>>
>>>>     
>>>>         
>>> You should be able to study interactions between individual molecules 
>>> by using energygrps and an appropriate index file.
>>>
>>> -Justin
>>>
>>>  
>>>       
>>>> Thanks.
>>>>
>>>> Darrell
>>>>