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.abra...@anu.edu.au <mailto:mark.abra...@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
    <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:

        On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote:


            Hi Mark

            I read the link before posting the question. even though
            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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
            <mailto:mark.abra...@anu.edu.au
            <mailto:mark.abra...@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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