[AMBER] aMD run

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Sun, 5 Jan 2025 18:09:03 +0530

Dear Experts,
I am trying to run aMD simulation using amber24. I set the following
parameters in the mdin file
iamd=1,
  ethreshp=-159511.27,
  alphap=8490.88,

aMD simulation runs properly. But when I visualize the trajectory I see the
following snapshotr of the protein.
Is this correct? If not, what can I do? How do I set the aMD parameter?

-- 
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*

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Received on Sun Jan 05 2025 - 05:00:02 PST