[AMBER] SHAKEH problem in GPU calculation

From: sangita kachhap <nckachap.cyf-kr.edu.pl>
Date: Tue, 21 Nov 2017 11:30:25 +0100

Dear AMBER developer

I have to do MD simulation of protein-metal ion employing bonded model. I
have generated topology file for bonded model. When I am using CPU for
calculations, its working fine. but when using GPU, its showing bellow
"3086: 6179 - 6180 and 3088: 6178 - 6180
Hydrogen atom 6180 appears to have multiple bonds to atoms 6179 and 6180
which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."

Atom 6180 is hydrogen of crystallized water molecule, I have included in
bonded model.
I also checked the protein-metal ion complex structure after 10 ns
production run, generated by CPU calculations and its looking fine.

So, please suggest me how to solve it.

With regards
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Received on Tue Nov 21 2017 - 03:00:02 PST
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