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

[Berk Hess]

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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