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
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
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
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