[gmx-users] Reg: NPT Equilibration of water

vinothkumar mohanakrishnan kmvinoth at gmail.com
Fri Oct 29 13:11:27 CEST 2010

```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?

Regards
Vinoth

On Fri, Oct 29, 2010 at 4:21 PM, Justin A. Lemkul <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>> 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
>>>
>>>
>>>               --
>>>               gmx-users mailing list gmx-users at gromacs.org
>>>            <mailto:gmx-users at gromacs.org>
>>>               <mailto:gmx-users at gromacs.org
>>>            <mailto:gmx-users at gromacs.org>>
>>>
>>>               http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>               Please search the archive at
>>>               http://www.gromacs.org/Support/Mailing_Lists/Search
>>>            before posting!
>>>               Please don't post (un)subscribe requests to the list.
>>>            Use the www
>>>               interface or send it to gmx-users-request at gromacs.org
>>>            <mailto:gmx-users-request at gromacs.org>
>>>               <mailto:gmx-users-request at gromacs.org
>>>            <mailto:gmx-users-request at gromacs.org>>.
>>>
>>>            http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>>        --         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>
>>> http://folding.bmc.uu.se
>>>
>>>
>>>        --         gmx-users mailing list    gmx-users at gromacs.org
>>>        <mailto:gmx-users at gromacs.org>
>>>        http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>        Please search the archive at
>>>        http://www.gromacs.org/Support/Mailing_Lists/Search before
>>>        posting!
>>>        Please don't post (un)subscribe requests to the list. Use the
>>>        www interface or send it to gmx-users-request at gromacs.org
>>>        <mailto:gmx-users-request at gromacs.org>.
>>>
>>>
>>>
>>
>>    --
>>    gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>    Please don't post (un)subscribe requests to the list. Use the
>>    www interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.