[gmx-users] Pressure Calculation in Gromacs

[Mark Abraham]

Hi,

That depends what your other inputs are. See the reference manual, chapter
2.

Mark

On Tue, Jul 17, 2018 at 5:05 AM Brandon Wiebe <Brandon.Wiebe at ufv.ca> wrote:

> Thank you, Justin.
>
> So if I wanted to simulate a system of Lennard-Jones particles under the
> NPT ensemble using reduced units, would I need to set ref_p to P*, or
> PRESFAC*(P*)?
>
> Regards,
> Brandon
> ________________________________________
> 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, July 16, 2018 7:23 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pressure Calculation in Gromacs
>
> On 7/16/18 9:55 PM, Brandon Wiebe wrote:
> > Hi there,
> >
> > I am wondering if anyone can break down exactly how the instantaneous
> pressure of any given frame is calculated in Gromacs?
> >
> > According to section 3.4.3 of the manual, the pressure tensor is given
> by: P = (2/V) * (Ek - W), where Ek is kinetic energy and W is the virial.
> > I have taken a particular frame and calculated the volume, kinetic
> energy and virial.
> > My calculated quantities all match quite closely with the values
> reported by Gromacs, however, the pressure that I get is significantly
> lower than the value reported by Gromacs.
> > The elements of my calculated pressure tensor are all approximately 16.5
> times smaller than those reported by Gromacs, even though the component
> quantities that go into the pressure calculation are nearly identical.
>
> There's a unit conversion factor (see src/gromacs/math/units.h):
>
> /* Pressure in MD units is:
>   * 1 bar = 1e5 Pa = 1e5 kg m^-1 s^-2 = 1e-28 kg nm^-1 ps^-2 = 1e-28 /
> AMU amu nm^1 ps ^2
>   */
> #define BAR_MDUNITS      (1e5*NANO*PICO*PICO/AMU)
> #define PRESFAC          (1.0/BAR_MDUNITS)
>
> PRESFAC works out to be 16.6.
>
> -Justin
>
> > I have repeated this calculation for a number of frames, and have tried
> using Gromacs 4.6.7 and 5.0.4 to no avail.
> > Clearly there is some systematic error in my methodology, where could
> this discrepancy come from?
> >
> > Regards,
> > Brandon
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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