Hi,
I would like to know if I run a 20ns MD simulation and save the trajectory
every 1ns, and so I have 20 separate trajectories (each is 1ns). Are these
20 trajectories consider as independent MD run?
>>>> These cannot be considered independent trajectories because you are merely saving them and not restarting your simulations (using ig=-1).
Instead, after equilibrations, you can run, as many as you wish, parallel simulations using ig=-1 and these will be considered independent trajectories. Even better if you start from slightly different starting points(conformations).
Second scenario:
If I extracted several structures from a single 20ns trajectory (say
structure at 5ns and 10ns) and use these structures to run another two 20ns
MD simulations (same parameter and setting as the previous 20ns
simulations), are these two 20ns simulations using structure at 5ns and
10ns as starting structure consider as independent MD run?
>> Yes here you can that.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: colvin <colvin4367.gmail.com>
Sent: 05 October 2017 08:41
To: AMBER Mailing List
Subject: [AMBER] Independent MD runs
Dear all.
I would like to know if I run a 20ns MD simulation and save the trajectory
every 1ns, and so I have 20 separate trajectories (each is 1ns). Are these
20 trajectories consider as independent MD run?
Second scenario:
If I extracted several structures from a single 20ns trajectory (say
structure at 5ns and 10ns) and use these structures to run another two 20ns
MD simulations (same parameter and setting as the previous 20ns
simulations), are these two 20ns simulations using structure at 5ns and
10ns as starting structure consider as independent MD run?
If not, what should I do to run an independent MD run?
Thank you!
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Received on Wed Oct 04 2017 - 22:00:03 PDT
