[gmx-users] pressure dependence on volume.

[Johnny Lu]

I saved .cpt file every minute. And using the xvg file generated by
g_energy, I picked the .cpt file with the volume that I want, and then run
a NVT simulation, continuing from thee NPT .cpt file.

The volume of the .cpt file of the NPT simulation should be same as the
volume of the NVT file. Is it so? Or manually setting the volume makes some
magical differences?

On Sun, Oct 19, 2014 at 10:24 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Thanks for answering my questions too.
>
> On Sun, Oct 19, 2014 at 10:18 AM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
>
>> The averaged volume of the 1bar pressure NPT simulation over 150ns was
>> very clearly 298.5 nm^3.
>> But now, when I set the volume of the NVT simulation to 298.7 nm^3 by
>> starting from a NPT frame that has the volume, the average was 1.2 bar with
>> error estimate 0.53, over 52 ns.
>>
>> The same tactic also didn't work for a 300 ns NPT simulation and
>> subsequently 300 ns NVT simulation. This NVT simulation pressure was
>> averaged to be around 4 bar.
>>
>> Why starting a NVT simulation from a NPT frame with the averaged NPT
>> volume didn't give the target pressure of 1 bar?
>>
>>
>>
>> On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>> wrote:
>>
>>> Hi Johnny,
>>>
>>> The density is M/V. The only parameter changing with pressure coupling is
>>> V, so the density and volume are fully correlated. No surprise there.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>> On Oct 19, 2014 2:27 AM, "Johnny Lu" <johnny.lu128 at gmail.com> wrote:
>>>
>>> > The frames with density closest to the average density also have
>>> volumes
>>> > closest to the averaged volume.
>>> >
>>> > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu <johnny.lu128 at gmail.com>
>>> wrote:
>>> >
>>> > > I searched the energy file made by g_energy, and found that NPT
>>> frames
>>> > > with very similar densities have very similar volume.
>>> > >
>>> > > So, I guess using density is same as using volume in this case.
>>> > >
>>> > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu <johnny.lu128 at gmail.com>
>>> > wrote:
>>> > >
>>> > >> Would manually setting the box size make vacuum bubbles?
>>> > >>
>>> > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu <johnny.lu128 at gmail.com>
>>> > >> wrote:
>>> > >>
>>> > >>> my bad. that formula for density is wrong. But I till don't see why
>>> > >>> using the same averaged density (instead of volume) for the NVT
>>> and NPT
>>> > >>> simulations would give a different result.
>>> > >>>
>>> > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu <johnny.lu128 at gmail.com
>>> >
>>> > >>> wrote:
>>> > >>>
>>> > >>>> Was the density calculated by # particles /  volume ?
>>> > >>>>
>>> > >>>> If so, using volume (as I did), and using density would give the
>>> same
>>> > >>>> wrong pressure, upon transitioning from NPT to NVT.
>>> > >>>>
>>> > >>>
>>> > >>>
>>> > >>
>>> > >
>>> > --
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>>
>>
>