[gmx-users] pressure dependence on volume.

[Johnny Lu]

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.
>> > >>>>
>> > >>>
>> > >>>
>> > >>
>> > >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>