Re: [AMBER] cpptraj: grid and gist

From: Jason Swails <>
Date: Tue, 8 Dec 2015 08:28:50 -0500

On Tue, Dec 8, 2015 at 8:15 AM, Thomas Fox <> wrote:

> Hi Steve -
> thanks for the fast response...yes, I would like to try the code if
> possible; I need to check if gist can replace some in-house written
> analysis
> software, and my colleagues are eagerly awaiting my verdict :-)
> Or should this better go through Dan so that your version is consistent
> with
> the most recent github version of cpptraj (which is the one I use)?
> I can certainly send you my example, although I inherited it from
> someone
> who obviously didnt really know how to run MD simulations properly -
> there
> are a number of vacuum bubbles in the trajectory which indicate poor
> equilibration of the box size before switching to NVT...but as an
> example to
> check if grid and gist give consistent results it should work
> nevertheless...dont know what would be the best way to transfer the
> trajectory though...
> My suggestion would be the following: if you send me the code I can try
> it
> out on my trajectory and see if the results are now as I would have
> expected
> them, and only if things still look weird we go through the hassle of
> moving
> the trajectory files.
> What do you think?

​Well if you follow the Github version of cpptraj, the PR with this change
seems to have already been made. You can either wait for that to be merged
or check out the PR branch directly.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Dec 08 2015 - 05:30:04 PST
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