[gmx-users] pressure and temperature coupling is off in vacuum simulations

[Mark Abraham]

Hi,

True, there can be cases where a vacuum simulation is a useful model of
reality. :-)

Mark

On Wed, Sep 23, 2015 at 12:38 PM Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

>
> On 23 Sep 2015, at 08:28, Mark Abraham <mark.j.abraham at gmail.com<mailto:
> mark.j.abraham at gmail.com>> wrote:
>
> Hi,
>
> On Wed, Sep 23, 2015 at 8:32 AM tasneem kausar <tasneemkausar12 at gmail.com
> <mailto:tasneemkausar12 at gmail.com>>
> wrote:
>
> Dear Gromacs users
>
> I have performed MD simulation for protein in vacuum condition.
>
>
> That's super artificial, so nothing else you do matters :-)
>
> This tongue-in-cheek reply does deserve a comment. Indeed the vacuum
> conditions introduce additional accuracy problems to the physical model,
> and one must be aware of this as to not over-interpret the results. A very
> fair point. That is not to say that we cannot learn from vacuum simulations
> of macromolecules however. Surely, the approach to, for instance, treat the
> protein as perfect ball also suffers from accuracy problems?! Or do you
> object to the notion of gas-phase proteins are artificial? Sure, it rarely
> happens in cellular processes (to my knowledge), but mass spectrometry is
> an extremely useful technique for the biosciences and requires gas-phase
> samples. As such experiments become more advanced (and they do, rapidly),
> there are more and more reasons to model the experiments. We do not know
> the objective here, and should not be so quick to dismiss the investigation.
>
> Erik
>
>
> I have seen
> papers where people are putting the pressure and temperature coupling off
> in mdp file. So I followed the same procedure. But I am not sure that what
> is the reason to put these (temperature and pressure coupling) off.
>
>
> They're choosing to sample a different ensemble. Perhaps because they're
> using non-periodic boundary conditions, and pressure coupling doesn't make
> any sense there.
>
>
> And
> what is happening to system by altering these parameters?
>
>
> It may be a better model of reality, inasmuch as a vacuum simulation models
> reality. :-)
>
> Mark
>
>
> If anyone having explanation about this please tell.
>
> Thanks and Regards
> --
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