[gmx-users] Re: gmx-users Digest, Vol 81, Issue 14

[Navjeet Ahalawat]

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