On 5/3/13 2:21 PM, James Starlight wrote:
Couple extra question about umbrella
Does it possible to use Collective variable (eigenvector from EDA or NMA)
as the pulling coordinate?
Does it possible to use output from essential dynamics sampling (here I can
use EDS in targeted mode to pull my st
Couple extra question about umbrella
Does it possible to use Collective variable (eigenvector from EDA or NMA)
as the pulling coordinate?
Does it possible to use output from essential dynamics sampling (here I can
use EDS in targeted mode to pull my structure to the target conformation)
for the um
On 4/30/13 1:38 PM, James Starlight wrote:
Justin,
could you also tell me
1) what difference should be expected from the umbrella sampling run with
(as I want to do for better coverage) and without (as in your tutorial)
velocities re-assignment on each umbrella window run ?
You have to dis
Justin,
could you also tell me
1) what difference should be expected from the umbrella sampling run with
(as I want to do for better coverage) and without (as in your tutorial)
velocities re-assignment on each umbrella window run ?
2) On what suggestions should I chose each conformer from pullin
On 4/30/13 10:58 AM, James Starlight wrote:
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
simulatio
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
simulations and N productions runs. In the tutorial I've
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