[gmx-users] Gentle heating with implicit solvent

[Mark Abraham]

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 :-)

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

> 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
>                     +1 (206) 685 4435
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>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
>                     http://healthynaturalbaby.org
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