[gmx-users] RE: tutorials for Coarse-Grained MD Simulation

[Justin Lemkul]

On 8/7/12 6:51 AM, J Peterson wrote:
> Thank you so much for clearing my doubt.
>
> I have another doubt that how can I use g_fg2cg program in reverse
> transformation (RT) while this program is not an internal GROMACS program.
>
> The RT tutorial in MARTINI website says that one has to compile and source
> the files from rev_trans.tar.gz.
> How do I do this step.?
>

Follow whatever instructions they provide for the installation.  It's probably 
just a modified version of Gromacs with an additional tool, so the installation 
would be like any you would do for a normal Gromacs distribution.  Make sure to 
set a proper installation path to avoid overwriting your existing Gromacs 
installation.

> These files are also tested with Gormacs 3.3.1 version, how do they work
> with recent versions of GROMACS?
>

They don't.  People have discussed this problem previously.  In theory, you 
could probably re-create whatever necessary input files (.top, .tpr, etc) under 
version 3.3.1 and process any trajectories created with more modern versions. 
Version 3.3.1 is ancient and there have been hundreds of bug fixes and feature 
enhancements since it came out.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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