[gmx-users] Re: Average box size

Mark Abraham mark.abraham at anu.edu.au
Thu Jan 6 08:06:34 CET 2011 


On 01/06/11, Navjeet Ahalawat  <navjeet0211 at gmail.com> wrote:
> 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...
> 


Please double check the contents of pr.gro are what you think they are. The simplest explanation is a file mismatch...


> 
> Read 12348 atoms
> 

Does that make sense?


> 
> 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
> 

I wondered if editconf was assigning mass to TIP4P vacant sites, but they'd have to have mass 13.1 per solvent molecule to make that work...

Mark


> 
> 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,
> 
> >The average lengths you already mentioned in your first mail:
> 
> >>>         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
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
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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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