# [gmx-users] Reg: NPT Equilibration of water

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 29 16:58:59 CEST 2010

```On 29/10/2010 7:50 PM, vinothkumar mohanakrishnan wrote:
> Hi Mark
>
> How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more
> clearly? It will be of more useful to me to understand the concept.

It's a pretty basic one in scientific measurement. See
http://en.wikipedia.org/wiki/Error_bar and links thereon, or an
introductory physics text.

When we make a measurement, that's only an estimate of the true value.
When someone cites a range of uncertainty, they are acknowledging that
there is an appreciable chance that the true value, of which they have
taken an error-prone measurement, lies somewhere in a given range. So if
7 +/-500 acknowledges that the true value could lie anywhere from about
-493 to 507, then that's not much less useful than an observation of 1
+/- 500, which acknowledges that the true value could lie anywhere from
about -499 to 501. The details of that chance will vary with exactly
what variation quantity is being reported (standard deviation, standard
error, maximum deviation, quartile, etc.).

Here, g_energy is effectively reporting that the instantaneous pressure
values varied over a range of many hundreds of bar, and that you haven't
made enough observations to report a reliable average.

Mark

>
> One more thing, density (from g_energy command) of water is found to
> low (expected 1000) after NPT is equilibration. why? given below is my
> average density value. Can i proceed with this density value?
>
> Energy                      Average       RMSD     Fluct.      Drift
> Tot-Drift
> -------------------------------------------------------------------------------
> Density (SI)                 979.37    14.3238    14.2431 -0.0525784
> -5.25789
>
> Regards
> Vinoth
>
> On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote:
>>     I am using the semiisotropic pressure scaling because i want the
>>     box size to remain the same as that of the original box size in X
>>     and Y axis and want to change it only on the Z axis. I am doing
>>     this because at a latter stage i want to create an interface with
>>     organic solvent where i need the cross sections (X and Y axis
>>     length) of both the box should be the same.
>>
>>     what i should do now  get the pressure of 1 bar?
>
>     7 +/- 500 *is* approximately 1 bar, and hardly any better an
>     approximation than 1 +/- 500. If you want lower fluctuations, use
>     a larger system and run for a much longer time. Or, since you'll
>     have to re-equilibrate once you combine the solvent boxes, don't
>     bother.
>
>     Mark
>
>>
>>     Has no one has got the pressure of water to be close to 1 bar in
>>     GROMACS till now?
>>
>>     Regards
>>     Vinoth
>>
>>     On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel
>>     <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>>
>>         On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote:
>>
>>
>>             Hi Mark
>>
>>             the fluctation
>>             is between 500-600 (as said in the link) bar the average
>>             pressure is
>>             around 7.4 bar. my concern is the average pressure?.
>>             Because at a latter
>>             stage i am going to combine this water box with another
>>             organic solvent
>>             and i want to avoid any complications there.
>>
>>
>>         Think again of what you just wrote. Your value is 7 +/- 500.
>>         In fact according to normal statistical rules you should
>>         round the value of 7 to 0. If you want more accurate number
>>         you could increase the box size by a factor of 100.
>>
>>         By the way, why are you using semiisotropic pressure scaling
>>         in a water box?
>>
>>
>>             Regards
>>             Vinoth
>>
>>             On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham
>>             <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>>             <mailto:Mark.Abraham at anu.edu.au
>>             <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>>
>>                On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote:
>>
>>                    Hi Gromacians
>>
>>                    I want to do equilibration of water (spc model)
>>             first in the NVT
>>                    ensemble and then in the NPT ensemble to maintain
>>             a temperature
>>                    of 300K and a pressure of 1 bar respectively. The NVT
>>                    equilibration works fine and the average
>>             temperature turns out
>>                    to be 299.229 K.
>>
>>                    Energy                      Average       RMSD
>>                Fluct.
>>                          Drift            Tot-Drift
>>                    ------------------------------
>>                    -------------------------------------------------
>>                    Temperature                 299.229    10.3092
>>              10.2463
>>                      0.0393873    3.93877
>>                    Heat Capacity Cv:       12.494 J/mol K (factor =
>>             0.00118698)
>>
>>                      when i do NPT equilibration i am not getting the
>>             desired
>>                    pressure as 1 bar or atleast close to 1 bar
>>             (between 1-1.4 bar).
>>                    In the mdp file i used semiisotropic pressure
>>             coupling type
>>                    because i want to fix the length of the box same
>>             on two axis as
>>                    that of the original box size and want to change
>>             it only on one
>>                    axis. can any one tell me why iam not getting the
>>             desired
>>                    pressure of 1 bar?.
>>
>>
>>                This looks normal for a smallish water system over
>>             100ps. See
>>             http://www.gromacs.org/Documentation/Terminology/Pressure
>>
>>                Mark
>>
>>
>>
>>                    Energy                      Average       RMSD
>>             Fluct.
>>                      Drift  Tot-Drift
>>
>>              -------------------------------------------------------------------------------
>>                    Pressure (bar)               7.4339    574.052
>>              573.574
>>                    0.812129    81.2138
>>
>>                    Given below is my mdp file (NPT equilibration).
>>             any help is
>>                    highly appreciated.
>>
>>                    title           = DCE NVT equilibration
>>                    cpp           = usr/bin/cpp
>>                    integrator   = md
>>                    nsteps       = 100000
>>                    dt              = 0.001
>>                    nstxout       = 100
>>                    nstvout       = 100
>>                    nstenergy   = 100
>>                    nstlog        = 100
>>                    ns_type     = grid
>>                    nstlist        = 1
>>                    rlist            = 1.0
>>                    coulombtype    = PME
>>                    rcoulomb         = 1.0
>>                    vdwtype          = Cut-off
>>                    rvdw               = 1.0
>>                    pme_order       = 4
>>                    fourierspacing  = 0.16
>>                    pbc                 = xyz
>>                    tcoupl              = V-rescale
>>                    tc-grps             = system
>>                    tau_t                = 0.1
>>                    ref_t                 = 300
>>                    pcoupl              = berendsen
>>                    pcoupltype        = semiisotropic
>>                    tau_p                = 0.5
>>                    ref_p                 = 1.0 1.0
>>                    compressibility   = 0.0 4.5e-5
>>                    DispCorr            = Enerpres
>>                    gen_vel             = yes
>>                    gen_temp          = 300
>>                    gen_seed          = 173529
>>
>>                    Regards
>>                    Vinoth
>>
>>
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>>         --
>>         David van der Spoel, Ph.D., Professor of Biology
>>         Dept. of Cell & Molec. Biol., Uppsala University.
>>         Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>         spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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