[gmx-users] Re: gmx-users Digest, Vol 81, Issue 14
navjeet0211 at gmail.com
Tue Jan 4 10:44:31 CET 2011
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>
> <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,
> 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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