[gmx-users] .dat file from gmx densmap does not match prescribed size

[Berk Hess]

A grid element

I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Wednesday, January 22, 2020 5:07 PM
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size


What do you mean by 'element'?

Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists.
Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file?

By the way, the simulation box is 47.72970  x 5.51140 x 35.37240 nanometers (if that may help understanding the issue).

Thanks,
Michele

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Berk Hess <gmx3 at hotmail.com>
Sent: 22 January 2020 16:49
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] .dat file from gmx densmap does not match      prescribed      size

How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit.

/Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele Pellegrino <micpel at kth.se>
Sent: Tuesday, January 21, 2020 5:16 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size

Hello,


I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting.

I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course:


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531


OR (equivalently):


gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01


In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553).

I am using GROMACS 2019.4?.


What am I doing wrong?


Thanks for your help.


Cheers,

Michele
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