Re: [AMBER] cpptraj: grid and gist

From: Thomas Fox <>
Date: Tue, 8 Dec 2015 17:50:15 +0100

   Ah, didnt check...youre right! And indeed, now the two commands

   grid grid.dx 20 1. 20 1. 20 1. gridcenter 20. -2. 50. :WAT.O
   gist gridcntr 20. -2. 50. griddim 20 20 20 gridspacn 1. out gist.out

   produce (with the difference of the absolute value due to density vs.
   absolute number)
   identical dx files, both for single

   The only thing missing now (hint: christmas is near!) would be the
   with the bincenter keyword in the grid command: the gist grid now also has
   the problem
   that for 20 increments one would need to write out 21 grid points per

   Thanks again for the fast help!

   Gesendet: Dienstag, 08. Dezember 2015 um 14:28 Uhr
   Von: "Jason Swails" <>
   An: "AMBER Mailing List" <>
   Betreff: Re: [AMBER] cpptraj: grid and gist
   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?
   â€‹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


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Received on Tue Dec 08 2015 - 09:00:03 PST
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