[gmx-users] Reg: NPT Equilibration of water

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 29 13:58:41 CEST 2010



vinothkumar mohanakrishnan wrote:
> Hi Justin
> 
> Thank you. One more question regarding the Compressibility value usage. 
> can i use the Compressibility value of water (4.5e-5) for the NPT 
> equilibration of organic liquids (say DCE)? Is it resonable?
> 
> It was said in the gromacs mailing archive that for all liquids one can 
> use the Compressibility value of water. 
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg01245.html)
> 

Yes, it's fine.  When a lead developer and the manual (section 3.4.9) indicate 
that it is true, I would have no reason to second-guess it...

-Justin

> Regards
> Vinoth
> 
> On Fri, Oct 29, 2010 at 4:42 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     vinothkumar mohanakrishnan wrote:
> 
>         Hi Justin
> 
>         Thank you for your comments. Yes i want to concatenate two
>         systems such that their cross sections are same ( X and Y axis
>         length are same for both the boxes) allowing only the Z axis to
>         change. The above procedure was employed in the literature and
>         latter they combined two boxes.
> 
>         what i want to know ultimately is can i go ahead with this
>         pressure ( i have no problem with temperature and density) for
>         water to create an interface by combining two boxes?
> 
> 
> 
>     Yes, it's fine.  Regardless, you're going to have to do more
>     equilibration after you've assembled the system.
> 
>     -Justin
> 
>         Regards
>         Vinoth
> 
> 
>         On Fri, Oct 29, 2010 at 4:21 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            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.
> 
> 
>            Suppose you do two simulations.  In one, the result is
>         7+/-500 and
>            in the other, the result is 1+/-500.  Even though the latter
>            achieves the preferred result (average pressure of 1 bar),
>            statistically, there is no difference between these two results
>            because of the huge standard deviations in the data.
> 
> 
>                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
> 
> 
>            Real water and SPC water are different.  I don't know that
>         there is
>            any water model out there that perfectly reproduces all the
>            properties of water.  A density around 980 sounds about right
>         for SPC.
> 
>            A comment on your previous approach: you're hoping to achieve the
>            same box dimensions for two different systems in order to
>            concatenate them and make an interfacial system?  It would be far
>            easier to create the organic phase, extend the box in z, and then
>            solvate with genbox.
> 
>            -Justin
> 
> 
>                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>
>         <mailto: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>
>                <mailto: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> <mailto:spoel at xray.bmc.uu.se
>         <mailto:spoel at xray.bmc.uu.se>>
>                    <mailto:spoel at xray.bmc.uu.se
>         <mailto:spoel at xray.bmc.uu.se> <mailto: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
> 
>                               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.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>>
>                    <mailto: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>>>
>                               <mailto: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>>
>                               <mailto: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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>            --     ========================================
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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