Dear David,
It is indeed due to a problem with the cuda version of pmemd.
Both cpu version of pmemd and sander report the effective born radii at the end of the output file.
Many thanks for your help.
Eric
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 23 October 2018 17:48
To: AMBER Mailing List
Subject: Re: [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file
On Tue, Oct 23, 2018, Eric Lang wrote:
>
> I am trying to get the effective born radii for each atom of a molecule
> when running implicit solvent calculations. For this I am using the
> rbornstat = 1 flag.
>
> However, it appears that the statistics for the effective Born radii is
> somehow not properly calculated, with MAX RAD = 0, MIN RAD =999 and AVE
> RAD and FLUCT =0. Here is what I obtain in my mdout file:
>
> I am using pmemd.cuda from Amber 16.
Try either the cpu version of pmemd, or sander. It is not unlikely that
the cuda version doesn't implement the rbornstat command. (Of course,
it should print out an error message if that is the case; but this is a
very rarely used command, and might have slipped by without anyone ever
noticing....)
....dac
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Received on Wed Oct 24 2018 - 02:30:02 PDT
