[gmx-users] Tc grps, one group or two?

[Mark Abraham]

On Thu, Jun 12, 2014 at 4:11 AM, 陈功 <gchen511 at gmail.com> wrote:

> Dear gromacs users,
>      I have doubts that whether I should use two groups to control the
> temperature or just one since there are just 604 hundred Protein beads and
> 60000+ solvent beads. It is said that two groups are more accurate but when
> when i split them into two groups "Protein nonProtein", I found that
> fluctulation of temperature in group "Protein" are obvious, Im afraid that
> would have an effect on accuracy on my simulation results.
>   Can anyone help me ?  thanks in advance
>

This is a complex issue. Even with a proper thermostat (i.e not Berendsen),
making a sound observation of temperature is tricky. See
http://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf
Measuring and managing temperature in the presence of other possible
problems (invalid or non-transferable force-field parameters,
non-conservative integration schemes) is even harder. Whether any of this
is relevant to your intended observables is usually unknown, because
typically no previous work was based on simulations sufficiently converged
to be definitive.

With orders of magnitude more solvent than solute, I would generally
suggest a single temperature-coupling group, but there may be issues with
how your coarse-grained force field was parameterized of which I am unaware.

Mark

regards,
> chen
>
>
>
>
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