[gmx-users] center of mass

Dear all i want to determine the center of mass of my protein in the z-dimension.which command in gromacs is useful for me? thanks Choose the right car based on your needs. Check out Yahoo! Autos new Car

[gmx-users] How to proceed with energy minimization for Normal Mode Analysis

Hi, I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. For that I require a well minimized structure. I have minimized my structure using steepest descent and conjugate gradient. But the structure seems to have got struct in a local energy minima. How should I proceed to g

Re: [gmx-users] OpenMosix and Gromacs

Nicolas Sapay wrote: Actually, I have used OpenMosix some time ago in a another life :) All I remember is that NAMD was performing reasonably well as far as you didn't ask it to write coordinates every frames. It was handy to minimize/equilibrate a system or do some small computation like press

Re: [gmx-users] How to proceed with energy minimization for Normal Mode Analysis

Anirban Ghosh wrote: Hi, I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. For that I require a well minimized structure. I have minimized my structure using steepest descent and conjugate gradient. But the structure seems to have got struct in a local energy minima. Ho

Re: [gmx-users] center of mass

mahbubeh zarrabi wrote: Dear all i want to determine the center of mass of my protein in the z-dimension.which command in gromacs is useful for me? thanks g_traj Choose the right car based on your ne

Re: [gmx-users] OpenMosix and Gromacs

OpenMosix indeed provides a second model for clustering besides beuwolf model, which uses MPI, PVM-based communication. You may run thousands of processes and get good scaling. I tried it with normal network, 100M Ethernet, two processes, quite bad efficiency, 1.1-1.3x speed-up. To get OpenMos

[gmx-users] pdb2gmx not recognizing disulfides

Hello, I'm having problems with pdb2gmx not recognizing disulfides in my protein. I've tried chaning the residue name and -ss flag but neither works. I read that this was a known bug on the website. Does anyone have a fix for this? Thanks, Russell Green ___

[gmx-users] pb with temperature in brownian dynamics

re Amber. Using that structure as the starting structure also, i got the same error i mention earlier. please suggest me something thanks -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION BANGALORE INDIA -- next part -- An HTML