[gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
Christian Blau
blau at kth.se
Thu Jan 23 13:30:11 CET 2020
Hi Michele,
Thanks for the input and suggestion!
I created a redmine issue using your observations that you can follow at
https://redmine.gromacs.org/issues/3353
Best,
Christian
On 2020-01-23 11:03, Michele Pellegrino wrote:
> Ok, I believe I have found the nature of this 'quirk' looking at the source code (as Berk suggested me to do).
> I was assuming a format, but GROMACS is producing another: the .dat file in the output contains the values PLUS the coordinates for each bin, that is the first row and the first colum are not denisty values, but coordinates; hence the output matrix is indeed (n1+1)x(n2+1), the actual values being in grid[1:n1-1,1:n2-1] (0-start index convention).
> So apparently is not a bug in the code, but just a misunderstanding of me as user; I double checked the documentation (both for 2019.04 and for the new 2020 release) and I did not find any reference to the format of the output file: could it be a good idea to incude some indication in that regard?
>
> Cheers,
> Michele
>
> * there is a typo in the original message (2:n2-2 instead of 1:n2-1)
> ________________________________________
> 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: 22 January 2020 22:58
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
>
> I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file.
> I managed to make it work by defining the number of values in each direction as (in Python):
> Nx = np.sqrt(Nda*Lx/Lz)
> Nz = Nx*Lz/Lx
> Nx = int( np.round(Nx) )
> Nz = int( np.round(Nz) )
> being Nda the number of values in the .dat file and Lx (resp. Lz) the lenght of the simulation box in the x (z) direction (np stands for numpy).
> However, I believe this manipulation should not be necessary.
>
> Cheers,
> 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 David van der Spoel <spoel at xray.bmc.uu.se>
> Sent: 22 January 2020 22:07
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
>
> Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino:
>> Ok, thank you.
>> I am counting the elements assuming they are in an array organized in a row major fashion.
> have you tried supplying -n1 47 -n2 35 to be able to check manually?
>
> (by the way a resolution of 0.1 Angstrom is unlikely to give you a
> smooth surface)
>> Scarica Outlook per Android<https://aka.ms/ghei36>
>> ________________________________
>> 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: Wednesday, January 22, 2020 6:34:47 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
>>
>> 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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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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