[gmx-users] Re:Re: Re: Average box size
Navjeet Ahalawat
navjeet0211 at gmail.com
Thu Jan 6 09:54:22 CET 2011
Hi Mark,
I have double check my pr.gro file It has 12348 atoms (129 protein
residues(1960 atoms)+ 2595 Tip4p-EW water molecules upto atom # 12340+
8 CL ions). My protein is Lysozyme, for water definition i have pasted
first and last water molecules.
File name: pr.gro
LYSOZYME in water
12348
...
...
...
130SOL OW 1961 1.516 0.734 1.474 -0.5687 0.1750 -0.1673
130SOL HW2 1962 1.565 0.744 1.392 0.7895 0.7537 0.6807
130SOL HW3 1963 1.521 0.821 1.514 -0.9351 -0.1981 0.6811
130SOL MW4 1964 1.522 0.745 1.469 -0.4629 0.1969 0.0136
...
...
...
2724SOL OW12337 -0.764 4.089 3.761 0.3226 0.7973 0.3069
2724SOL HW212338 -0.744 4.179 3.787 -0.5681 1.1240 -0.1194
2724SOL HW312339 -0.743 4.086 3.668 1.3356 0.2670 0.5421
2724SOL MW412340 -0.760 4.099 3.754 0.3356 0.7753 0.2868
...
...
2732Cl Cl12348 0.340 3.555 3.399 -0.4800 0.0112 -0.0034
4.44372 4.49672 4.88141 0.00000 0.00000 -1.83507 0.00000
-1.53659 -0.46242
Please tell me (if required) any other way(s) by which I can calculate
the mass of my system.
Thanks & Regards,
Navjeet Ahalawat
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
> >> --
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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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