[gmx-users] Reg: NPT Equilibration of water

vinothkumar mohanakrishnan kmvinoth at gmail.com
Fri Oct 29 10:50:13 CEST 2010


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.

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>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> 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>> 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    http://folding.bmc.uu.se
>>
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