[gmx-users] Average box size

[Tsjerk Wassenaar]

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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