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 <tsje...@gmail.com> > Subject: Re: [gmx-users] Average box size > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <aanlktik2tyhljvmvfc12260rqkdznuge-3kokigfb...@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" <navjeet0...@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@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
