[gmx-users] Reg: NPT Equilibration of water
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Fri Oct 29 13:21:05 CEST 2010
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)
Regards
Vinoth
On Fri, Oct 29, 2010 at 4:42 PM, Justin A. Lemkul <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>> 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>>> 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>>>
>>
>> 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>>>> 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
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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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