<DIV> Dear Mark,</DIV>
<DIV>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!</DIV>
<DIV>All the best,</DIV>
<DIV> </DIV>
<DIV>Qinghua</DIV>
<DIV> </DIV>
<DIV> </DIV><PRE>> Date: Wed, 14 Apr 2010 00:09:16 +1000
> From: Mark Abraham <Mark.Abraham@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@gromacs.org>
> Message-ID: <4BC47B0C.4020208@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</PRE>