[gmx-users] restraints or constraints over two molecules

hi, i want to ask if there is a possibility to make distance restraints or contraints over two molecules? till now i have two .itp files (one for each molecule) and i include them with 'inculde ...itp . after that i have [ system ] and [ molecules ] (with my two molecules) and then [

RE: [gmx-users] restraints or constraints over two molecules

Hi, We still need an elegant solution for this problem. Currently the only option is to merge the two moleculetype definitions into one. Or if you are also happy with an harmonic restraint, you can use the pull code. Berk. Date: Wed, 2 Apr 2008 15:53:19 +0200 From: [EMAIL PROTECTED] To:

[gmx-users] B factor and R factor

Hi, What do B factor and R factor mean ? And what can be indicated fome them? -- Lu Shuai ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Error gmxtest

Dear All, I have compiled fftw3_3.0.1 in a specific user directory; then configured, compiled gromacs-3.3.2 according to directions and installed it in the specific directory, all without any errors, but at the end make tests command fails, the output is: (if test -d gmxtest; then cd gmxtest;

Re: [gmx-users] Error gmxtest

Nadia Gro wrote: Dear All, I have compiled fftw3_3.0.1 in a specific user directory; then configured, compiled gromacs-3.3.2 according to directions and installed it in the specific directory, all without any errors, but at the end make tests command fails, the output is: (if test -d

[gmx-users] topolbuild 1.1, update to an all-atoms model gromacs topology generator

I've made a number of changes to topolbuild to correct problems, and improve the results. Version 1.1 is now available in the user contributions at the gromacs web site. The following revisions are included: 1. Scaled Tripos out of plane bending parameter to derive better improper dihedral

[gmx-users] how to calculate the RMSD of the peptide conformation relative to the NMR structure?

Dear everyone, Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Thanks again! Fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] how to calculate the RMSD of the peptide conformation relative to the NMR structure?

Quoting [EMAIL PROTECTED]: Dear everyone, Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Thanks again! Try g_rms -h -Justin Fufeng Liu ___ gmx-users mailing list

[gmx-users] how to put two rmsd plot in one plot

Dear all, I need two rmsd plots(protein and the ligand) , and I want use one plot display them, How can I do it? Thank you in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] how to put two rmsd plot in one plot

Rui Li wrote: Dear all, I need two rmsd plots(protein and the ligand) , and I want use one plot display them, How can I do it? Please describe better. Mark ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how to put two rmsd plot in one plot

You mean 2 plots ? one above the other ? Or all this data on the same plot ? On Thu, Apr 3, 2008 at 1:27 AM, Mark Abraham [EMAIL PROTECTED] wrote: Rui Li wrote: Dear all, I need two rmsd plots(protein and the ligand) , and I want use one plot display them, How can I do it? Please