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

fancy2012 fancy2012 at yeah.net
Wed Apr 14 02:54:45 CEST 2010

 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!
All the best,
> 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
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