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 <navjeet0...@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 <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-us...@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 > -- 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 -- 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
