Re: [AMBER] Multiple Replicate Trajectories

From: Adrian Roitberg <>
Date: Wed, 3 Nov 2021 09:46:53 -0400

It depends...

irest=1,ntx=5 will pick up coordinates AND velocities from the initial
structure. This means you start your MD at the right temperature, and
then ig=1, ntt=3 will create a different random number sequence for each
runs, which will make them "independent".

irest=0, ntx=1 with ntt=3, ig=1 will also make them independent, but now
the initial velocities will be random, and there is a small chance that
the initial T would be different than your request target. This is not
crucial, since it goes to the proper one reasonably fast.


On 11/3/21 9:40 AM, Li,Haoxi wrote:
> [External Email]
> Dear Amber Users,
> I was planning to run multiple replicate production trajectories from the same equilibrated structure. Can I use the same input file (with ig=-1 and ntt=3) for all the replicate simulations? Do I need to change other options, like set ntx=1 or irest=0? Thank you in advance!
> Best,
> Haoxi
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
AMBER mailing list
Received on Wed Nov 03 2021 - 07:00:03 PDT
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