[gmx-users] lipid parameters for ffG43a1

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 22 11:55:51 CET 2008

pragya chohan wrote:
> Hello users
> Is there anyone running simulation of lipid bilayers in ffG43a1 or any other force field apart from ffgmx?

> Could anyone tell me how to compile a patch into already installed Gromacs . I have 3.3 in my system and want to comile a patch for secondary structure prediction.

A non-expert can't sensibly modify an existing gromacs installation.

A correct approach to replace the installation would be to uninstall the 
existing GROMACS, get the correct source distribution, unpack it, apply 
the patch, and then use configure in the same way as the original 
installation, plus any patch-specific things, then make and install

A superior approach is probably to make a second gromacs installation 
with the patch applied, since it's likely that you will not want to use 
this patch for all of your GROMACS work. Leave your existing 
installation, get the source, unpack, patch and then when you configure, 
have a look at "./configure --help" and choose a judicious combination 
of "./configure --prefix=/your/choice/of/location 
--program-suffix=_yoursuffix" and your usual configuration options, then 
make and install. Now you have the option of sourcing the GMXRC from 
/your/choice/of/location from your working shell when you want the 
patched executables to be used, and you can be sure which version is 
being used because you'll have to supply the suffix. For normal usage, 
you just source the normal GMXRC in your .bashrc/.cshrc/whatever. This 
also has the effect of isolating your normal GROMACS usage from any bugs 
that the patch might introduce, which is an important consideration.


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