[gmx-users] glutamic acid protonation

Hi group. I am having a sudden brainfart here and apologize for the silliness of the question. If the first amino acid of your protein is a Glutamic acid, what would you set the protonation status using the -ter option of pdb2gmx? The protein is in 0.1 molar NaCl solution. I know it is basic Bi

[gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.

Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than Berendsen for this pur

[gmx-users] mdrun_mpi issue.

Hi Folks, I am trying to run a simulation under GMX 4.0.5. When I do a qsub of my job, it does not seem to run and gives me an error saying the library libimf.so is not available. I tried subsequently giving/copying the library into the run path with still the exact same error. I am attaching th

[gmx-users] Forcefields and water models for protein simulations.

Dear All, I recently asked a question about comparing the forcefields for protein simulations and the appropriate water model to use for the same to which Justin answered back. Thanks for the answer justin.   In addition, I found a couple of references which I think are really good for the above

[gmx-users] Questions about protein simulations.

Dear Gromacs users, Hi I wanted to ask a begnniner's question regarding protein MD. I have prior experience with MD simulations through simulating lipid systems. However I beginning to do some protein MD simulations and wanted the anyone's advice regarding the forcefields to be used for proteins

[gmx-users] Extracting a sub-trajectory

Hi Group, I had a question regarding the extraction of the trajectory of a specific subset of atoms. In a simulation of water molecules surrounding ions, If I wanted to analyse properties of a subset of water molecules which are WITHIN a specified DISTANCE surrounding the ion, how do I go about