Re: [AMBER] Wanting to get synchronized trajectory files

From: Abdullah Bin Faheem <>
Date: Wed, 22 Jan 2020 15:05:28 +0000

Thank you for your response. While using 100 steps produces the same coordinates, noticeable deviations in the coordinate file begin to appear after 3000 steps. Is it not possible to run longer trajectories? Say 50 or 100 ps without experiencing changes.

From: David Case <>
Sent: Wednesday, January 22, 2020 10:09 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Wanting to get synchronized trajectory files

On Wed, Jan 22, 2020, Abdullah Bin Faheem wrote:
>Is it possible to get the same output trajectory file if I use the same
>topology and restart file?
>Meaning if I run two MD runs in parallel, can I get the same xyz (or
>atleast very close) coordinates being written in the output coordinate
>file if I use the same restart and topology file? This is the input file
>I used initially (I am currently using AMBER 12):

What happenes when you tryrunning (say) two 100-step simulations?
Don't be afraid to experiment. Be sure to set ig (I'm not sure what the
default value for that was way back in 2010.)


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Received on Wed Jan 22 2020 - 07:30:04 PST
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