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.castebla...@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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