I advise against heating from zero in any case. the details depend a
bit on the thermostat type, etc, but I think it can still be dangerous
to ramp the temperature too much. an extreme example is with a
Berendsen thermostat- if part of the system is a bit high in energy
when you start, even if it is in a local minimum, it can result in
very hot sections of the system. for example, if you start at 10K and
a side chain was strained and picks up just a little extra kinetic
energy , say enough to put it at 50K, then when you scale the bath to
300K, the 50K part gets scaled to 1500K. If you start at 100K and part
is 50K hotter, then it's not nearly as bad a problem.
ramping the temperature by a large factor in a short run requires a
really good thermostat and good coupling between various parts of the
simulated system (which can be worse in GB, which may be why you were
advised to be especially careful there).
On Thu, Nov 27, 2008 at 1:29 PM, Francesco Pietra <chiendarret.gmail.com> wrote:
> For GB, I was recently advised to start heating up the system to 300K
> from about 100K, not from 0K. Now that I am back to explicit
> environment for a protein complex (25,000 atoms) partly in a lipidic
> membrane, and the whole in TIP3BOX (68,000), where I was used to
>
> nmropt=1
> /
> &wt type='TEMP0', istep1=0,istep2=35000,
> value1=0.0, value2=300.0
> /
> &wt type='END'
> /
>
> does a similar warning as for GB applies here too?
>
> Thanks
> francesco pietra
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 18:04:48 PST
