[gmx-users] Continuing a FEP alchemical
alexanderwien2k at gmail.com
Wed Dec 28 17:24:51 CET 2016
Thank for your response.
You mean for the TI analysis, now problem if one .xvg file (e.g.
case.3.xvg) has just 15 columns while another .xvg file (e.g. case.18.xvg)
has 20 columns? and still the "alchemical analysis package" could be used
to calculate the free energy change via TI method?
On Wed, Dec 28, 2016 at 5:12 PM, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk
> On Wed, 28 Dec 2016 16:40:49 +0100
> Alex <alexanderwien2k at gmail.com> wrote:
> > Hello Gromacs user,
> > I have a free energy simulation converged results harvested by
> > alchemcial analysis in 15 lambada windows, now, I would like to
> > increase the number of lambada windows to 20. Would you please let me
> > know how I can continue my old simulation with 15 windows to 20
> > windows?
> Just add the additional lambda points to your lambda vector and run
> the simulations for those. For TI analysis this is all you need to do.
> For FEP style analysis you would need to make sure that you also have
> the energy projections for the neighbouring lambda(s). You should be
> able to use the -rerun feature to compute those (but think about
> nstxout != nstdhdl).
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