[gmx-users] Reg: NPT Equilibration of water
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Oct 29 16:58:59 CEST 2010
On 29/10/2010 7:50 PM, 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.
It's a pretty basic one in scientific measurement. See
http://en.wikipedia.org/wiki/Error_bar and links thereon, or an
introductory physics text.
When we make a measurement, that's only an estimate of the true value.
When someone cites a range of uncertainty, they are acknowledging that
there is an appreciable chance that the true value, of which they have
taken an error-prone measurement, lies somewhere in a given range. So if
7 +/-500 acknowledges that the true value could lie anywhere from about
-493 to 507, then that's not much less useful than an observation of 1
+/- 500, which acknowledges that the true value could lie anywhere from
about -499 to 501. The details of that chance will vary with exactly
what variation quantity is being reported (standard deviation, standard
error, maximum deviation, quartile, etc.).
Here, g_energy is effectively reporting that the instantaneous pressure
values varied over a range of many hundreds of bar, and that you haven't
made enough observations to report a reliable average.
Mark
>
> 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
> <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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>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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