Try running for longer and look at the convergence of the temperatures
over time. I suspect that what you are reporting is actually just
statistical noise.
I am not sure about using the sd integrator and defining multiple
temperature coupling groups... If you define the same temperature for
each then I suspect this is the exact same as defining the system as a
single temperature coupling group (for the sd integrator).
Since you can not extract dynamic information from your FE simulations
anyway, the sd integrator is the best choice.
Chris.
-- original message --
Hi there,
I am also doing FEP calculations and I am also using sd as integrator.
The problem that I am having with this integrator is the temperature
coupling (NTP). I am setting the targeted temperature of the system on
300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me
303K 301K respectably.
If I use the md and noose-hover thermostat the results are 300K for
both groups. For that reason I was thinking on changing to md. But
afther reading the post
http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html
I think that I shuold stick on sd. The questions are
If by trying sd with target temperature 298K and get 300K as a result,
is the simulation valid?
Fabian, If you use sd the temperature of your system is the wanted one?
Thanks in advance
Marcelino
Justin A. Lemkul <jalemkul at vt.edu> wrote:
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