[gmx-users] Re: How to prepare the two tolopogy files when doing TI calculation?

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 14 03:14:37 CEST 2010

fancy2012 wrote:
>  Dear Mark,
> I know that the tutorial can go through, my problem is just how to 
> generate the two topology files. From the tutorial, I know how to run TI 
> calculation, but first, I got to know how to prepare these files, both 
> for topology and coordinate files. I will highly appreciate for your 
> suggestion if you can help me! Thanks!

Be advised that calculating free energies in Gromacs-4.0.x is different from the 
instructions in the tutorial, which are for version 3.3.x; topology manipulation 
is no longer necessary and the methods for decoupling are controlled by settings 
in the .mdp file.  You haven't said which version of Gromacs you're using, but 
that is quite important.  There are several threads in the list archive that 
discuss free energy calculations in Gromacs-4.0.x.  There are no tutorials, 
however.  There are various programs in the User Contribution section of the 
Gromacs site for generating small molecule topologies, as well as the PRODRG 
server for Gromos topologies.  The parameters that any of these programs give 
are not necessarily 100% reliable (especially in the case of PRODRG).

Generating a coordinate file is going to depend on what you're doing.  If you 
have a simple small molecule in water, you'll have to have some initial 
configuration for the solute and there are many tools that can be used for that 
purpose.  Solvent can be added with genbox.  But since you haven't given any 
details of what it is that you're trying to accomplish, that's about as precise 
as any advice can get.


> All the best,
> Qinghua
>> Date: Wed, 14 Apr 2010 00:09:16 +1000
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] How to prepare the two tolopogy files when
>> 	doing	TI	calculation?
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4BC47B0C.4020208 at anu.edu.au>
>> Content-Type: text/plain; charset=x-gbk; format=flowed
>> On 13/04/2010 7:35 PM, fancy2012 wrote:
>> > Dear GMX users,
>> > I want to do some TI calculation using GMX, and I have learned the
>> > tutorial of TI calculation from this web site
>> > http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial.
>> > So I have know how to run TI calculations. But there is still a problem.
>> > I don't know how to prepare the two topology files, which are initial
>> > and final states, respectively. Could somebody give me some suggestion
>> > on it? Any response will be highly appreciated! Thanks!
>> Didn't the tutorial go through that? Look at its examples.
>> Mark


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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