# [gmx-users] Re: Average box size

Navjeet Ahalawat navjeet0211 at gmail.com
Thu Jan 6 07:38:55 CET 2011

```Hi Tsjerk,

Thanks for your more clarification, but when I am running the command
editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro
is end.gro) the results I am getting are...

Volume: 97.5411 nm^3, corresponds to roughly 43800 electrons
Velocities found
system size :  7.244  4.992  5.194 (nm)
center      :  0.534  2.027  2.438 (nm)
box vectors :  4.444  4.857  5.138 (nm)
box angles  :  88.30 107.40 112.20 (degrees)
box volume  :  97.54               (nm^3)
Volume  of input 97.5411 (nm^3)
Mass    of input 95417.2 (a.m.u.)
Density of input 1624.38 (g/l)
Scaling all box vectors by 1.1589
new system size :  8.395  5.785  6.019
new center      :  0.618  2.349  2.825 (nm)
new box vectors :  5.150  5.628  5.955 (nm)
new box angles  :  88.30 107.40 112.20 (degrees)
new box volume  : 151.82               (nm^3)

This new box volume is not matching with my average box volume
(97.6118). I think problem is with mass because my system (box)
contains 1 protein, 2595 water molecules(Tip4p-EW),and 8 CL ions. So
the total mass should be 61307.332 a.m.u. (14313.332+18*2595+8*35.50)
and when I am calculating the density using this mass and average
volume (97.6118), its coming 1042.94 g/l which is approximately same
to average density (1.04364e+03).

I would greatly appreciate if you could please let me know why
editconf is giving mass different from actual mass (my calculated
mass).

Thanks & Regards,
Navjeet Ahalawat

>Navjeet,

>>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03

>You also mentioned you used isotropic PC:

>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling.

Then the box only gets scaled during the simulation, with no changes
of one vector relative to the other. Then to set the box of your end
structure to match the average volume also means scaling. That means
taking the ratio of the average X-length and the actual X-length, and
feed that as a scaling factor...
Then again, you don't actually need to calculate anything, just think
a little bit harder. You're average box comes with an average density.
editconf has an option to scale the box to get a specific density, so
you can fetch the average density, given above and do:

editconf -f end.gro -o average.gro -density 1.04364e+03

Then go on with your NVT run using average.gro as input (don't forget
the energy minimization!).

Hope it helps,

Tsjerk

On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
> Hi Tsjerk,
>
> Thanks for your clarifications. I still couldn't follow how I can calculate
> the scaling factor. As I wrote earlier, I ran NPT simulation for equilibration.
>
> Now to start the NVT production run, I need to know the AVERAGE LENGTHS
> (a, b, c) of the triclinic box vectors so that I can generate the
> triclinic box with the
> help of the corresponding angles (88.30, 107.40, 112.20) using the
> command "editconf".
>
> Now I understand that the box-x, box-y, and box-z represents the diagonal
> elements of triangular matrix and the average volume of my triclinic box
> is the product of these diagonal elements. However, as I understand the
> command "editconf" requires the length of the box vectors and the three angles
> to create a triclinic box.
>
> I would greatly appreciate if you could please let me know the command(s) that
> I would require to use to achieve my goal.
>
>
>
>
> Message: 4
> Date: Tue, 4 Jan 2011 12:35:36 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Re: Average box size
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <AANLkTimMYai39NMj6sv008zUuVpT_UHZAvHm=tAH34yK at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Navjeet,
>
> These you had in the log file as you showed in your mail. Note that
> you use isotropic pressure coupling, so you just need to calculate a
> scaling factor, which you can give to editconf to change your system
> to match the average box size.
>
>  Cheers,
>
> Tsjerk
>
> On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
>> Hi Tsjerk,
>>
>> Thanks for reply, Please can you tell me how can I get the average box
>> length (a b c) of my triclinic box for my next step.
>>
>>> Message: 2
>>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>>> Subject: Re: [gmx-users] Average box size
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID:
>>>        <AANLkTik2TYHLJVmVFC12260RqkdZnUGe-3kOKigFbM3h at mail.gmail.com>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Hi Navjeet,
>>>
>>> The box is defined as a triangular matrix, so the volume equals the product
>>> of the diagonal elements.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat" <navjeet0211 at gmail.com> wrote:
>>>
>>> Hi all
>>>
>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>>> average box size for production run (NVT). But I am confused because i
>>> am not able to get the meaning of the output values of the log file.
>>>
>>>
>>> Log file output.....
>>>
>>>       <======  ###############  ==>
>>>       <====  A V E R A G E S  ====>
>>>       <==  ###############  ======>
>>>
>>>  Energies (kJ/mol)
>>>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>>>   9.31715e+02    2.35558e+03    1.63083e+02    5.15266e+03    1.79003e+03
>>>    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>>>   1.63211e+04    2.86765e+04   -1.72320e+05   -4.98704e+04   -1.66800e+05
>>>   Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
>>>   1.27874e+04   -1.54012e+05    1.49958e+02    1.07033e+00    0.00000e+00
>>>
>>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
>>>
>>> If Box-X Box-Y Box-Z represent average value of  a b c then volume
>>> does not correspond to my triclinic box because its just
>>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
>>> which volume should I consider for next NVT production run.
>>>
>>> Any help in this regard would be highly appreciated.
>>>
>>>
>>> Thanks & Regards,
>>> Navjeet Ahalawat
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
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