Navjeet, We're stuck with the information you give us. Apparently something's not entirely adding up, or not matching with the way editconf calculates the density. But don't break your head about it. I gave another solution: calculate a scaling factor and use that with editconf. That's completely independent of mass.
Cheers, Tsjerk On Thu, Jan 6, 2011 at 9:54 AM, Navjeet Ahalawat <[email protected]> wrote: > Hi Mark, > > I have double check my pr.gro file It has 12348 atoms (129 protein > residues(1960 atoms)+ 2595 Tip4p-EW water molecules upto atom # 12340+ > 8 CL ions). My protein is Lysozyme, for water definition i have pasted > first and last water molecules. > > File name: pr.gro > > LYSOZYME in water > 12348 > ... > ... > ... > 130SOL OW 1961 1.516 0.734 1.474 -0.5687 0.1750 -0.1673 > 130SOL HW2 1962 1.565 0.744 1.392 0.7895 0.7537 0.6807 > 130SOL HW3 1963 1.521 0.821 1.514 -0.9351 -0.1981 0.6811 > 130SOL MW4 1964 1.522 0.745 1.469 -0.4629 0.1969 0.0136 > ... > ... > ... > 2724SOL OW12337 -0.764 4.089 3.761 0.3226 0.7973 0.3069 > 2724SOL HW212338 -0.744 4.179 3.787 -0.5681 1.1240 -0.1194 > 2724SOL HW312339 -0.743 4.086 3.668 1.3356 0.2670 0.5421 > 2724SOL MW412340 -0.760 4.099 3.754 0.3356 0.7753 0.2868 > ... > ... > 2732Cl Cl12348 0.340 3.555 3.399 -0.4800 0.0112 -0.0034 > 4.44372 4.49672 4.88141 0.00000 0.00000 -1.83507 0.00000 > -1.53659 -0.46242 > > Please tell me (if required) any other way(s) by which I can calculate > the mass of my system. > > Thanks & Regards, > Navjeet Ahalawat > > > On 01/06/11, Navjeet Ahalawat <[email protected]> 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 <[email protected]> >> 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 <[email protected]> >> > Subject: Re: [gmx-users] Re: Average box size >> > To: Discussion list for GROMACS users <[email protected]> >> > Message-ID: >> > <[email protected]> >> > 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 <[email protected]> >> > 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 <[email protected]> >> >>> Subject: Re: [gmx-users] Average box size >> >>> To: Discussion list for GROMACS users <[email protected]> >> >>> Message-ID: >> >>> <[email protected]> >> >>> 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" <[email protected]> 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 [email protected] >> >> 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 [email protected]. >> >> 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 [email protected] >> > 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 [email protected]. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110106/5acc42a6/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 81, Issue 35 > ***************************************** > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
