[gmx-users] Free Energy Integrator Selection

Fabian Casteblanco fabian.casteblanco at gmail.com
Mon Aug 22 19:06:06 CEST 2011

Dear all,

I was running free energy calculation for a drug molecule in solvent.


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?

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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