[gmx-users] Adsorption energy of a single molecule

[Mark Abraham]

Darrell Koskinen wrote:
> 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?

I don't know what Justin suggested, but a re-run with each ammonia in 
its own energy group ought to allow you to observe absorption events 
from the individual energy profiles over time.

Mark

>> 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
>>>>>         
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