[gmx-users] Free Energy Integrator Selection

[chris.neale at utoronto.ca]

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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