[gmx-users] Using GPU to do simulations

Hi everyone, I am trying to do some pulling simulations by gromacs (i.e., pull a ligand from its binding site), as the system is large I want to accelerate the simulations by GPU. I want to confirm that, Does GPU simulation support the pulling code of GROMACS? Can I use GPU acceleration to do

[gmx-users] calculation speed of GROMACS and cut off parameters

Hi everyone, I am using GROMACS to simulate bilayers, and I am testing two sets of parameters at present. However, I found significant differences of simulation speed of these two parameters sets. The mainly differences between these parameters are the cut off parameters or of the VDW and coul

[gmx-users] calculating block average and error estimate by g_analyze tool in gromacs

Hi All: I am using g_analyze to analyze my data and I want to do error estimate by blocking averaging. However, I encountered some problems of understanding the output results. THe command i used was: g_analyze -f input.xvg -ee output.xvg The input files are like this: 0 6.37011

[gmx-users] about thermal intergation calculations

Hi All: I am trying to do free energy calculations by thermal integration method and I have read the tutorials on the gromacs web site, they are really nice tutorials and help me a lot. But I still have two questions here: 1, After we define the necessary paramteres in the mdp file (such as the