Hi,
I'm having difficulty with a membrane receptor simulation. It seems like
whenever the receptor crosses the boundary (I'm using PBC), the box gets
distorted so that the z axis is compressed from 10.2nm to 8-8.2nm which is
too large a change.
I was initially using System for the comm-grps optio
On 5/23/14, 2:51 PM, Steve Seibold wrote:
My protein breaks according to viewing the traj in VMD and graphing the RMSD of
the protein C-terminus
I have tried all combinations of "trjconv -pbc -center
-box center" and nothing works..I was able to get online and find a
tutorial that says trjco
My protein breaks according to viewing the traj in VMD and graphing the RMSD of
the protein C-terminus
I have tried all combinations of "trjconv -pbc -center
-box center" and nothing works..I was able to get online and find a
tutorial that says trjconv -pbc mol, should stop the problem, but th
> > Hello everyone!
> >
> > I am a new one of gromacs. When a simulation of protein in water is
> > finished,
> > should i first use the command of trjconv to remove pbc conditions(with
> > nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some
> > other parameters)? Is the r
On 3/4/14, 8:35 PM, 申昊 wrote:
Hello everyone!
I am a new one of gromacs. When a simulation of protein in water is finished,
should i first use the command of trjconv to remove pbc conditions(with
nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some
other parameters)? I
Hello everyone!
I am a new one of gromacs. When a simulation of protein in water is finished,
should i first use the command of trjconv to remove pbc conditions(with nojump
or mol), and then began analyze the new trajectory(rmsd, Rg and some other
parameters)? Is the result believable without
