On 01/06/11, Navjeet Ahalawat <navjeet0...@gmail.com> wrote: > Hi Tsjerk, > > Thanks for your more clarification, but when I am running the command > editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro > is end.gro) the results I am getting are... >
Please double check the contents of pr.gro are what you think they are. The simplest explanation is a file mismatch... > > Read 12348 atoms > Does that make sense? > > Volume: 97.5411 nm^3, corresponds to roughly 43800 electrons > Velocities found > system size : 7.244 4.992 5.194 (nm) > center : 0.534 2.027 2.438 (nm) > box vectors : 4.444 4.857 5.138 (nm) > box angles : 88.30 107.40 112.20 (degrees) > box volume : 97.54 (nm^3) > Volume of input 97.5411 (nm^3) > Mass of input 95417.2 (a.m.u.) > Density of input 1624.38 (g/l) > Scaling all box vectors by 1.1589 > new system size : 8.395 5.785 6.019 > new center : 0.618 2.349 2.825 (nm) > new box vectors : 5.150 5.628 5.955 (nm) > new box angles : 88.30 107.40 112.20 (degrees) > new box volume : 151.82 (nm^3) > > This new box volume is not matching with my average box volume > (97.6118). I think problem is with mass because my system (box) > contains 1 protein, 2595 water molecules(Tip4p-EW),and 8 CL ions. So > I wondered if editconf was assigning mass to TIP4P vacant sites, but they'd have to have mass 13.1 per solvent molecule to make that work... Mark > > the total mass should be 61307.332 a.m.u. (14313.332+18*2595+8*35.50) > and when I am calculating the density using this mass and average > volume (97.6118), its coming 1042.94 g/l which is approximately same > to average density (1.04364e+03). > > I would greatly appreciate if you could please let me know why > editconf is giving mass different from actual mass (my calculated > mass). > > Thanks & Regards, > Navjeet Ahalawat > > > > >Navjeet, > > >The average lengths you already mentioned in your first mail: > > >>> Box-X Box-Y Box-Z Volume Density (SI) > >>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03 > > >You also mentioned you used isotropic PC: > > >>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30, > >>> 107.40, 112.20) and Isotropic pressure coupling. > > Then the box only gets scaled during the simulation, with no changes > of one vector relative to the other. Then to set the box of your end > structure to match the average volume also means scaling. That means > taking the ratio of the average X-length and the actual X-length, and > feed that as a scaling factor... > Then again, you don't actually need to calculate anything, just think > a little bit harder. You're average box comes with an average density. > editconf has an option to scale the box to get a specific density, so > you can fetch the average density, given above and do: > > editconf -f end.gro -o average.gro -density 1.04364e+03 > > Then go on with your NVT run using average.gro as input (don't forget > the energy minimization!). > > Hope it helps, > > Tsjerk > > On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat <navjeet0...@gmail.com> > wrote: > > Hi Tsjerk, > > > > Thanks for your clarifications. I still couldn't follow how I can calculate > > the scaling factor. As I wrote earlier, I ran NPT simulation for > > equilibration. > > > > Now to start the NVT production run, I need to know the AVERAGE LENGTHS > > (a, b, c) of the triclinic box vectors so that I can generate the > > triclinic box with the > > help of the corresponding angles (88.30, 107.40, 112.20) using the > > command "editconf". > > > > Now I understand that the box-x, box-y, and box-z represents the diagonal > > elements of triangular matrix and the average volume of my triclinic box > > is the product of these diagonal elements. However, as I understand the > > command "editconf" requires the length of the box vectors and the three > > angles > > to create a triclinic box. > > > > I would greatly appreciate if you could please let me know the command(s) > > that > > I would require to use to achieve my goal. > > > > > > > > > > Message: 4 > > Date: Tue, 4 Jan 2011 12:35:36 +0100 > > From: Tsjerk Wassenaar <tsje...@gmail.com> > > Subject: Re: [gmx-users] Re: Average box size > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: > > <aanlktimmyai39nmj6sv008zuuvpt_uhzavhm=tah3...@mail.gmail.com> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > 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-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 > -- > 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 > >
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