[gmx-users] range of magnitude for force constant

Hi, I have rather elementary questions regarding force constants used in restraining position/orientation: - I have imposed a force with constants kx, ky, and kz =10^6 kJ/mol/nm^2 on a particular atom of a peptide to harmonically position restrain the molecule inside a bilayer. Is it a

[gmx-users] Amber port for GROMACS 4.0

Hi All, I was wondering how I can aquire AMBER ports for GROMACS4.0? Considering the ports given in (http://chemistry.csulb.edu/ffamber/) are suitable for version 3.3.3 and older. Noting the FAQ (http://chemistry.csulb.edu/ffamber/FAQ.html): - Can I use these ports with any version of GROMACS?

Re: [gmx-users] [ angle_restraints_z ]

Dear Berk, Thanks for the reply. Yes. In fact I made the choice of multiplicity=1 based on the explanation in eq. 4.68: "A multiplicity (n) of 2 is useful when you do not want to distinguish between parallel and anti-parallel vectors." Since my molecule is slightly polar and it may matter whet

[gmx-users] [ angle_restraints_z ]

Hi all, There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component: a1: atom#22 (x1,y1,60.231) a2: atom#45 (x2,y2,60.231)If I use these lines only Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous MD runs the a1-a2 were flexible (the

[gmx-users] viewing .xvg plots in windows environment

Hi, I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP environment. Can anyone please suggest a good way to do this? -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] which tpr?

Hello all, Because of the limitations in run time, my simulations have broken into three parts: one.trr, two.trr, and three.trr. Each run has its corresponding tpr file. The original tpr file (minimization step) was start.tpr. Now using trjconv for three.trr which tpr file I need to type after -s