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

[Erik Marklund]

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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