[AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential

From: Zuo, Zhicheng <Zhicheng.Zuo.unthsc.edu>
Date: Thu, 21 Jun 2018 21:45:16 +0000

The recently released AMBER18 adds GPU support for 12-6-4 ion potentials.
I did some tests, and found that it did works for the case where an ion is treated
traditionally as a single point charge with the 12-6-4 LJ potential. However, for the simulation
of the recent multisite ion (dummy atom) model with the 12-6-4 potential (https://pubs.acs.org/doi/10.1021/acs.jpclett.7b02358),
I got the following error from pmemd.cuda:
"Too many hydrogens for a hydrogen network, exiting."

Interestingly, there is no any problem with the cpu version of pmemd for the 12-6-4 multisite ion model above.

It seems that this issue is related to implementation of pmemd.cuda toward such a special divalent ion model.
Can someone help to figure it out? Thanks!

Zhicheng Zuo
Postdoc research associate from College of Pharmacy,
UNT Health Science Center, Fort Worth, TX, USA.

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Received on Thu Jun 21 2018 - 15:00:02 PDT
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