[gmx-users] Pressure and box volume

[Mark Abraham]

Hi,

Look at the simulation box volume over time. You can't start making
measurements of pressure at equilibrium until that converges, but
fortunately the volume is less noisy. Then you need a large amount of data
to observe that the average pressure matches the external pressure because
of the massive fluctuations in the former. (Look at a plot of pressure over
time.) Whether that will happen at a desirable volume depends on the
quality of the underlying model.

Mark

On Mon, 20 Mar 2017 16:55 Mishelle Oña <samimishu at hotmail.com> wrote:

> Hello Justin,
>
> Thanks for your response. I made the following steps before the pressure
> error happened:
>
> 1)Built a system of 1 polymer (30 monomer)
>
> 2)Run EM simulation in vaccum
>
> 3) Add solvent (water)
>
> 4) Run a EM simulation with the solvated system
>
> 5) Run a relaxation simulation
>
> 6) Run a NVT simulation
>
> 7) Run NPT simulation (when the problem occured)
>
> It is supposed that NVT simulation stabilizes temperature and it actually
> does. Then NPT simulation is used to stabilize the pressure but this did
> not happend. I run a 500 ps and the a 5000 ps simulation and it still has
> the same pressure of 300 bar aprox.
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: Monday, March 20, 2017 6:54 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pressure and box volume
>
>
>
> On 3/19/17 8:42 PM, Mishelle Oña wrote:
> > Hello Justin!
> >
> > I was trying to getting down the pressure of my simulation from aprox
> 300 bar to 1 bar. I increased the box volume and now I have 27 bars but my
> density decrease dramatically from 970 to 320 kg/m3. I tried to add more
> water molecules to increase it again but then the pressure scaled up to 300
> bar again. To make a production simulation we should equilibrate the
> parameters of Temperature, Pressure, density and Volume. Should I continue
> playing with the size of the box and the amount of water molecules until I
> get all this parameters acording to the conditions I want or is anything
> else I can do instead?
> >
>
> "Randomly toying with box size and water content" is not a reproducible
> method :)
>
> We're missing a lot of context here, like everything you've done up to this
> point, so it's really hard to comment.  But in general, it is certainly not
> necessary to make all these ad hoc changes.  You may just have to wait a
> while
> for the pressure to stabilize, depending on how far from equilibrium your
> initial state was (and it sounds like it was pretty far from your desired
> value).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
> http://mackerell.umaryland.edu/~jalemkul>
>
> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
> mackerell.umaryland.edu
> Welcome to my site! To learn more about me and the work I am doing, please
> use the navigation links above.
>
>
>
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> GMX-Users List - Gromacs<
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
> www.gromacs.org
> This is the main discussion forum for users of GROMACS and related
> software. Subscribe, unsubscribe or change your preferences through
> gmx-users Admin page.
>
>
>
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists>
> www.gromacs.org
> The three mailing lists (see the menu items on the left) have slightly
> different purposes, and you might not be interested in subscribing to all
> of them:
>
>
>
>
> * 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.org_gmx-users Info Page - Royal Institute of ...<
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> maillist.sys.kth.se
> gromacs.org_gmx-users -- Discussion list for GROMACS users About
> gromacs.org_gmx-users
>
>
>
> --
> 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.
>