Re: [AMBER] TI simulation blowing up with pmemd.CUDA

From: Delwakkada Liyanage, Senal Dinuka <>
Date: Sun, 10 Jan 2021 20:08:21 +0000

Hello Dr. Case,

The unit cell dimensions are as 52.981 x 42.118 x 52.650 angstroms and the amber 18 version have been updated to the latest. There wasn't any issue during the decharging step throughout the lambda values. So, I'm unsure as to why a sudden energy burst should happen at the second lambda point simulation for vdW removal.

Following is the terminal output I obtained from running my script on the CPU code.

simulating vdw_bonded
changing directory to lambda = 0.00922
equilibration for 350 ps
equilibration for 1 ns
sampling for 10 ns
changing directory to lambda = 0.04794
equilibration for 350 ps
equilibration for 1 ns
sampling for 10 ns
Error: an illegal memory access was encountered launching kernel kNLSkinTest

Thank you

Senal Liyanage
From: David A Case <>
Sent: Sunday, January 10, 2021 1:28 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] TI simulation blowing up with pmemd.CUDA

On Sun, Jan 10, 2021, Delwakkada Liyanage, Senal Dinuka wrote:
>I am trying to do TI in Amber18 with pmemd.cuda. The system is a small
>porphyrin ligand ( C44H38N8), prepared in a 16 A TIP3P water box.

What are the unit cell dimensions for your system? Small systems can be
unstable with with our GPU code, but I'm not sure when the relevant error
message was inserted into the code.

For sure, be certain that you have applied all updates to the code. If it's
not something obvious, you will probably need to upgrade to Amber20: there
have been significant changes in how softcore TI is done, and not all of the
fixes have been back-ported to Amber18.


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Received on Sun Jan 10 2021 - 12:30:02 PST
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