[gmx-users] Plumed

[jkrieger at mrc-lmb.cam.ac.uk]

Dear Alex,

There are a wide range of methods available in Plumed for free energy
calculation and enhanced sampling. I think the main benefit is the
collective variable based analyses such as metadynamics and umbrella
sampling. It also has ways of combining these with e.g. parallel tempering
and other replica exchange methods for further enhanced sampling. Whether
you need these methods or are happy with what's implemented in GROMACS
alone depends on what you want to do.

It's not too difficult to link them though. The one thing that's a bit
annoying for linking to GROMACS 5 is a duplicate reference to Plumed.o
from build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt, which you
have to remove. Here's my workflow for it, which works for patching Plumed
2.1.3 to GROMACS 5.0.4:
https://groups.google.com/forum/#!topic/plumed-users/stlK9-kaa6A

The step of adding to -fPIC to CFLAGS is no longer necessary as that was
fixed in Plumed 2.1.3 but otherwise you can follow the steps and it works.
You probably also want to set the suffixes in cmake with
-DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_mod -DGMX_LIBS_SUFFIX=_mod
changing mode to whatever you want to distinguish the plumed version from
another version. That said GROMACS with Plumed can perform GROMACS-only
runs absolutely fine so you could just make your Plumed version(s) your
dominant version(s).

Best wishes
James

> Dear Gromacs user,
>
> Before spending time on linking Gromacs to Plumed and learning it in order
> to do free energy calculations, I was wondering if Plumed does something
> extra more than our normal free energy calculation, FEP, or PMF in Gromacs
> or if it makes life easier in order to do these staff respect to the
> normal
> methods in Gromacs? In another word what is the necessity for it, if there
> is any?
>
> Thanks,
> Regards,
> Alex
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