[gmx-users] Free Energy Integrator Selection

[Justin A. Lemkul]

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

-- 
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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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