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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