[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
>>>
>>> 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>>> 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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>>> Dept. of Cell & Molec. Biol., Uppsala University.
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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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