[gmx-users] Pressure Question

[Johnny Lu]

the protein has about 170 amino acid.

On Wed, Nov 5, 2014 at 1:13 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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