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

From: David A Case <>
Date: Sun, 10 Jan 2021 14:28:09 -0500

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.


AMBER mailing list
Received on Sun Jan 10 2021 - 11:30:02 PST
Custom Search