[gmx-users] Pressure Question

[Johnny Lu]

The statistics was calculated for 80 ns of NVT simulation, after a 80 ns
NPT simulation.

In papers, I saw people talked about using the average volume of a previous
NPT simulation to choose the frame with the correct volume. And then, run
NVT starting from the NPT frame.
But they don't talk about the pressure that they get in the NVT simulation
(even in a force field paper).

I just want to know if the reviewer will be ok with my paper, if I mention
the pressure that I get in the NVT simulation.


On Wed, Nov 5, 2014 at 12:16 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> That's hard to say. You'd need to do multiple converged simulations at each
> set of conditions to know. First, make sure you've made a significant
> observation of the pressure.
>
> Mark
>
>
> On Tue, Nov 4, 2014 at 6:00 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > Hi.
> >
> > If my NVT simulation of a protein in 30k molecules of water has a
> pressure
> > of 11 bar (error 0.5 bar from g_energy), will the dynamics (not
> > distribution of conformations) change enough that the mechanism inferred
> > from this simulation be significantly more unreliable than the mechanism
> > inferred from a 1 bar simulation? (Will the reviewers cut my paper into
> > ribbons?)
> >
> > Thanks again.
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