[gmx-users] Adsorption energy of a single molecule

[Mark Abraham]

Darrell Koskinen wrote:
> Hi Justin,
> So when I create the index file with the molecule and the graphene sheet 
> and run g_energy, is the adsorption energy between the adsorbed molecule 
> and the graphene sheet the LJ (SR) energy?

Not necessarily, unless the force field was parameterized to produce 
such values. First, seek to define what you mean by adsorption (free) 
energy, then consider how a simulation might measure that. Then, 
consider whether any force fields exist that might achieve that. Then, 
test it on a case where you have experimental data.

Other procedures run a much higher risk of producing an expensive random 
number generator :-)

> And will this energy be just 
> the interaction energy between the adsorbed molecule and the graphene 
> sheet (i.e. does the creation of the new index file and executing -rerun 
> cause g_energy to exclude the energies between the other molecules and 
> the graphene sheet)?

Creating an energy group causes mdrun -rerun to report the fraction of 
the total nonbonded energies that are due to intra- and inter-group 
interactions. See manual section 3.3

Mark

>> Date: Sun, 01 Nov 2009 21:27:19 -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: <4AEE4387.40607 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> Darrell Koskinen wrote:
>>  
>>> Hi Justin,
>>> Since I cannot use the original .tpr file, then do I need to run 
>>> grompp with the new index file to create a "new" .tpr file, 
>>> "mdtopolnew.tpr"? I assume I then need to modify the energygrps line 
>>> within the .mdp file to include these new energy groups and then 
>>> execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct?
>>>
>>>     
>>
>> Yes, that is the point of the -rerun function.
>>
>>  
>>> Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a 
>>> molecular dynamics simulation to run once again? If so, then will the 
>>> exact same molecules that adsorbed on the first MD run be the same 
>>> ones that adsorb on the second MD run?
>>>
>>>     
>>
>> The original coordinates are used to re-calculate the energies.  No 
>> new simulation is performed.
>>
>> -Justin
>>
>>  
>>> Thanks.
>>>
>>> Darrell
>>>
>>> ***********************************************************************
>>> ***********************************************************************
>>>
>>>
>>> Date: Sun, 01 Nov 2009 19:29:36 -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: <4AEE27F0.50301 at vt.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>>
>>>
>>> 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?
>>>>      
>>>>>           
>>> Almost.  You can't use the original .tpr file if you are trying to 
>>> establish new energy monitoring groups.  Hence the point of making a 
>>> new .mdp file.  So, re-run the old trajectory with the new .tpr file 
>>> to take advantage of the new groups.
>>>
>>> -Justin
>>>
>>> -- ======================================== Justin A. Lemkul Ph.D. 
>>> Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia 
>>> Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 
>>> ========================================
>>>