[gmx-users] g_energy -fee -f2

[David]

On Sat, 2003-09-20 at 01:49, Ilya Chorny wrote:
> How does on run a trajectory using a tpr file from another trajectory?
> 

mdrun -rerun

> 
> Thanks
> 
> Ilya
> 
> On Thu, 2003-09-18 at 23:16, Anton Feenstra wrote:
> > Xavier Periole wrote:
> > > 
> > > You ractually have to run two simulations. One would be the reference state
> > > (A)
> > > and the other is the perturbated state (B). g_energy calculate the free
> > > energy difference
> > > between the two states A and B. G_energy does not generate the perturbation.
> > 
> > The way I have used this option is to look at free energy differences
> > in conformations between a ground-state (GS) and excited-state (XS)
> > fluorophore (FAD). In this case I ran two simulations, one with GS charges
> > on the FAD, and one with XS charges. Then, I did four re-runs: GS trajectory
> > with GS tpr, GS traj with XS tpr, XS traj with GS tpr and XS traj with FS tpr.
> > (The 'GS traj/GS tpr' and 'XS traj/XS tpr' re-runs seem unnecessary, but
> > there are slight differences in total energies calculated between 'original'
> > and 're-run' that are elminated when all energies come from re-runs.)
> > This gives an estimate of the delta-delta-G, i.e. the difference in free
> > energy difference between two transitions (e.g., GS charges -> XS charges in
> > one ensemble, or GS ens. -> XS ens. in one charge state).
> > 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++