[gmx-users] Free Energy Integrator Selection

[Marcelino Arciniega Castro]

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:


> 
> 
> Fabian Casteblanco wrote:
> 
> > Dear all,
> > 
> > I was running free energy calculation for a drug molecule in solvent.
> > 
> > First,
> > 
> > For [coulomb + vdW] --> [vdW] ,  I used 'md' integrator
> > 
> > For [vdW] --> [none],  I was using 'md' but it required me to switch
> > to 'sd' based on this error message:
> > 
> > "WARNING:  For proper sampling of the (nearly) decoupled state,
> > stochastic dynamics should be used.  "
> > 
> > Is using sd really much more accurate? Is it best to use 'sd' for
> > [coulomb + vdW] --> [vdW] as well?
> > 
> > 
> > 
> 
> Yes.  See, for instance, some of the commentary here:
> 
> http://lists.gromacs.org/pipermail/gmx-users/2007-February/025815.html
> 
> There are other posts regarding this topic, but I don't have the time to pull 
> them up.
> 
> -Justin
> 
> 
> > Thank you.
> > 
> > --
> > Best regards,
> > 
> > Fabian F. Casteblanco
> > Rutgers University --
> > Chemical Engineering PhD Student
> > C: +908 917 0723
> > E:  fabian.casteblanco at gmail.com
> > 
> > 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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