Re: [gmx-users] Trajectory: reducing

Alessandro Mattozzi wrote: Hi all is it possible to process a trajectory so to get the reduced trajectory with a predifined reducing timestep T? I.e. averaging the positions every T? If you don't want averaging then you can use trjconv, obviously. Given that trajectory snapshots adjacent in t

[gmx-users] RE:water molecules

Hi Beniamino, If it's not a VMD Problem and you simulations crashes, I have also seen such problems, the solution is use smaller time step or use SETTLE/SHAKE to constrain the O-H bond in water. Rahul ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] re: need help with free energy of solvation calculation

This is a follow-up from my post in January regarding my attempts to reproduce some free energy of solvation calculations for modified cellulose oligomers. First, a question: I know that certain values of sc-alpha are preferred for different cases, but are there any values that definitely shoul

Re: [gmx-users] Trajectory: reducing

Alessandro Mattozzi wrote: Hi all is it possible to process a trajectory so to get the reduced trajectory with a predifined reducing timestep T? I.e. averaging the positions every T? Regards Alessandro g_rmsf produces averages over a trajectory. You probably have to run a script. Alessand

[gmx-users] Trajectory: reducing

Title: Trajectory: reducing Hi all is it possible to process a trajectory so to get the reduced trajectory with a predifined reducing timestep T? I.e. averaging the positions every T? Regards Alessandro  Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal I