Re: [AMBER] GIST hydration analysis of big interface

From: Steven Ramsey <>
Date: Fri, 7 Oct 2016 11:31:39 -0400

Hi again,

Sorry for the double post, I noticed that in your command you are also
using the optional flags doorder and doeij, these calculations will likely
use a fair amount of memory as well. If these data are not integral to your
analysis you may want to omit them (which will both increase your runtime
and reduce memory usage).

Another comment that may be helpful is that entropies in GIST are currently
not calculated in the outer layer, so if you run several overlapping
regions of GIST keep in mind that your overlap should be by one voxel. The
concatenation of GIST output should be a tractable code to write, so long
as the GIST grids line up, which is to say the edge of one voxel overlaps
with the edges of a voxel in your second output, if they do not overlap
perfectly the combination becomes much more complex.

Hope this helps,


On Fri, Oct 7, 2016 at 10:56 AM, Steven Ramsey <> wrote:

> Hi Sergey,
> That sounds like a really interesting system to analyze! You are
> absolutely right that GIST can run into memory issues, but depending on
> when the crash is occurring (early vs late), there may be another issue at
> play. If the crash occurs after some time likely GIST is running out of
> memory as you suggest and kills itself.
> One suggestion would be to try the version of GIST in the cpptraj github,
> which has been upgraded and will run faster. If the crash you are
> experiencing is a bug and not memory related then the github version may
> have already addressed said bug...only one way to find out!
> Your intuitive solution of dividing and recombining GIST boxes is
> absolutely correct and would be my suggestion on how to tackle large
> regions of interest in the case of limited memory. Unfortunately GistPP
> does not have a function that combines two GIST outputs in the manner that
> would work with this fix, however it is definitely something that I'll
> implement in the future.
> The last comment I'd make is that there is a known bug regarding
> arbitrarily high energies when a trajectory is aligned prior to running
> GIST, therefore if at all possible it would be better to avoid using rms on
> a trajectory before using GIST.
> Hope this helps, best of luck,
> --Steve
> On Fri, Oct 7, 2016 at 10:22 AM, Sergey Samsonov <
>> wrote:
>> Dear AMBERs,
>> I'm trying to calculate hydration properties of a relatively big
>> interface between two macromolecules. Because the interface that
>> interests me consists of quite an extended H-bonding network (made up of
>> direct and water-mediated H-bonds) I'd like to apply GIST calculations
>> in the box containing the whole interface and, then, to get hydration
>> properties around the residues establishing this H-bonding network. To
>> do this I can use GistPP in the way it is shown in the tutorial.
>> However, I face a technical problem, which was previously already
>> partially discussed in the Mailing List: when I run GIST in a big box, I
>> get an error probably due to the memory shortage:
>> ------------------------------------
>> 1: [gist doorder doeij gridcntr 62 69 60 griddim 60 60 60 gridspacn
>> 0.5 out Region3/gist.out]
>> GIST number of voxels: 216000, voxel volume: 0.125000 A^3
>> GIST grid origin: 47.000 54.000 45.000
>> ./ line 1: 12480 Killed cpptraj
>> ../../ < gist3.ptraj
>> ------------------------------------
>> The same script starts to work without any problem when I decrease the
>> box sizes to 45 45 45 and still does not work if I just take
>> significantly less frames (I even tried with just one frame to check if
>> this could work) from the trajectory for my analysis.
>> I guess an intuitive way to overcome this obstacle is to split the
>> interface into several smaller boxes that do not yield problems for GIST
>> calculations, to cary out calculations for them and then to unite them.
>> The technical question is if it is possible to take two overlapping
>> boxes and unite them into one using GistPP?
>> Maybe I'm doing something wrong with my trajectory: prior to the
>> analysis I image the trajectory using a script containing centering and
>> rms to the the solute, and imaging with 'image center familiar' command.
>> Could this be a source of the error in following GIST calculations?
>> Thank you very much in advance and cheers,
>> Sergey
>> --
>> Sergey A. Samsonov
>> Postdoctoral researcher
>> Structural Bioinformatics
>> Biotechnology Center
>> Tatzberg 47-51
>> 01307 Dresden, Germany
>> Tel: (+49) 351 463 400 83
>> Fax: (+49) 351 463 402 87
>> E-mail:
>> Webpage:
>> _______________________________________________
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Received on Fri Oct 07 2016 - 09:00:03 PDT
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