[gmx-users] Fwd: Broken chain / fragmentation

Dear Gromacs users, My Gromacs simulation on a protein terminated without any error and major warning. However, when I see the conformations, I found them broken. For trajectory conversion, I have used the following commands: gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump

[gmx-users] Simulating a protein dimer

Dear Gromacs Users, I am trying to simulate a protein dimer using Gromacs-5.1.2. Gromacs completed successfully but when analysing the trajectories, the monomers are flying apart and coming back again! I used the following Gromacs commands/options: gmx trjconv -s protein-md.tpr -f

[gmx-users] Fragmented backbone

Dear Gromacs users/experts I was doing principal component analysis with a long (1000 ns) MD trajectory. I have seen the protein backbone continuous (not fragmented) with the simulation time. However, the backbone is fragmented in some trajectories corresponding to some of the eigenvectors! The

[gmx-users] RMSD reproducibility

Dear Gromacs Users, I have the following question: Suppose I repeat a simulation, keeping everything exactly the same. What will happen to RMSD? Will it be exactly same with the previous run? If not, then how much variation is expected? To check this, I ran two independent simulations: 1) upto

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 165

with time Message-ID: 5564dbb9.8020...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 5/26/15 8:42 AM, Biplab Ghosh wrote: Dear Gromacs Users, I am new to Gromacs and using Gromacs-5.0.4. I want to calculate the variation of distance between to C-alpha

[gmx-users] Variation of distance between 2 CA atoms with time

Dear Gromacs Users, I am new to Gromacs and using Gromacs-5.0.4. I want to calculate the variation of distance between to C-alpha atoms in a protein in course of time. First, I have created a file called: L153_V161.ndx using make_ndx and the content of the file is: [ L153 ] 2277 [ V161 ] 2394

[gmx-users] MD simulation of metalloprotein

Dear All, I am a beginner in MD and started with Gromacs. I would like to simulate the dynamics of a homo-dimeric protein containing 2 Mn atoms at the active site. I would appreciate any sorts of help in this regards, e.g., please share your experience and/or relevant source in the web/published