I see. Thanks.
Qing
At 2015-07-11 05:07:27, Justin Lemkul jalem...@vt.edu wrote:
On 7/9/15 11:00 PM, Qing Lv wrote:
It means to evaluate quantities over successive blocks of time (e.g. using
-b and -e that all GROMACS analysis tools support) and check to see whether
or not the
On 7/9/15 11:00 PM, Qing Lv wrote:
It means to evaluate quantities over successive blocks of time (e.g. using -b
and -e that all GROMACS analysis tools support) and check to see whether or not
the quantities of interest are varying over time or if they are stable, i.e.
converged.
Thank
Thank you, Justin.
I am trying to simulate a protein-ligand complex to see the conformation
transition during the simulation... We propose that the receptor pocket may be
subject to a conformational change upon ligand-binding, so I want to verify it
by MD...
I am really a newbie in molecular
On 7/9/15 10:11 AM, Qing Lv wrote:
Thank you, Justin.
I am trying to simulate a protein-ligand complex to see the conformation
transition during the simulation... We propose that the receptor pocket may be
subject to a conformational change upon ligand-binding, so I want to verify it
by
It means to evaluate quantities over successive blocks of time (e.g. using -b
and -e that all GROMACS analysis tools support) and check to see whether or
not the quantities of interest are varying over time or if they are stable,
i.e. converged.
Thank you, Justin.
What size of blocks I
Hi,
I did a 70-ns MD simulation. I wonder how to justify when the trajectory
reached equilibrium...
Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and
kept stable after that. Could I justify that the system reached equilibrium at
12 ns? Are there any
Hi,
I did a 70-ns MD simulation. I wonder how to justify when the trajectory
reached equilibrium...
Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and
kept stable after that. Could I justify that the system reached equilibrium at
12 ns? Are there any
