Re: [AMBER-Developers] Oddities in runmd.F90 in pmemd

From: Duke, Robert E Jr <>
Date: Thu, 13 Dec 2012 19:40:01 +0000

Hmmm, all past my tenure on pmemd itself, as I expect you know. I am buried in the amoeba code for right now, but will be interested in going back to see what happened to pmemd in the time period I have not been working on it when I get time. I would think the origin of npt could be tracked down, and I would agree it is not the correct way to fix a typo... It did not exist in Amber 10. Scott?
- Bob
From: David A Case []
Sent: Thursday, December 13, 2012 5:54 AM
Subject: [AMBER-Developers] Oddities in runmd.F90 in pmemd

(1) about the problem that occurs when ntr=1, ntp=1 on GPU:

   In the CPU code, when ntp>0 and ntr=1, there is a call to
   pressure_scale_restraint_crds(). But there is no gpu equivalent to this.
   Assuming that the restraint coordinates acutally used are the ones on the
   gpu(?), this looks like an error.

(2) There are several places where a specific if has been commented out,
   and replaced with a generic else: e.g. at about line 1257:

      !else if (npt .gt. 2) then

   Is there a reason for this? the effect of the above changes is that
   the following section is run even when ntp = 0, which looks wrong. Is it
   just that "npt" above is a typo (should be "ntp"), and was fixed in a
   funny way? Similar thing happens (but with no typo) for the csurften==3


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Received on Thu Dec 13 2012 - 12:00:03 PST
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