[gmx-users] Adsorption energy of a single molecule

[Justin A. Lemkul]

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 
> ========================================
> 
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-- 
========================================

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

========================================