[gmx-users] Gentle heating with implicit solvent

Mark Abraham mark.j.abraham at gmail.com
Wed Aug 28 09:16:09 CEST 2013

It can be. Lack of explicit degrees of freedom of solvent can make
achieving equipartition tricky. With CHARMM27 and virtual sites in implicit
solvent, I have sometimes found it necessary to use a sub-femtosecond time
step at the start of equilibration, even where there were no atomic
clashes. Maybe the system was just unlucky with generating velocities,
though :-)

On Aug 28, 2013 7:16 AM, "Gianluca Interlandi" <gianluca at u.washington.edu>

> How important is it to do gentle heating (using simulated annealing) with
> GBSA? Often with explicit water it is enough to perform some equilibration
> with positional restraints. Would it be enough to do the same with implicit
> solvent?
> Thanks,
>      Gianluca
> ------------------------------**-----------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
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> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
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