[AMBER] Question about equilibration of membrane protein MD

From: <m15295783798.163.com>
Date: Mon, 9 Jul 2018 17:14:56 +0800 (CST)

Dear Amber!

I'm running a membrane protein MD of my own complex following the Lipid14 tutorial with amber16 pmemd.cuda. I got the error message "ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values..." after about 800ps during equilibration. I know that I can restart the calculation using the latest restart file to continue the 10ns equilibration. However, it is not very convenient for me to do this automatically on the computer cluster, and it's too slow to run on cpu. So, I'm wondering if it's safe for me to split the whole 10ns equilibration into something such as 500ps*20, or should I restart the calculation as few as possible?

Thank you in advance.
Jingxiao Bao
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Received on Mon Jul 09 2018 - 02:30:01 PDT
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