[gmx-users] A possible bug in gmx density?

[Ganesh Shahane]

Dear Gromacs Users,

I have been trying to calculate the electron density profile of a lipid
bilayer using gmx density (gromacs version 5.1).

All is well and good when I use the following flags in my gromacs gmx
density command:

-ei to input the file containing atom types and their respective number of
electrons,
-center to perform binning relative to center of the box
-sl to divide the box in slices

...and this gives me a nice electron density profile of the said bilayer:

https://drive.google.com/file/d/0B2cmuCsErAPZaWF3TFFTUjRJMkE/view?usp=sharing

However the Y-axis of this graph has a scale is in Kg m^-3 and I wish this
to be in electron densities (e nm^-3).

Towards this, I tried to use the -dens flag with "electron" as the option,
along-with the above mentioned additional flags and then gromacs throws an
error:

"Invalid line in datafile at line 1"

This error I believe corresponds to the datafile that I input with -ei
flag. The format seems to be correct because gmx density works without the
-dens flag. The format of the file is as follows:

264
  OW=8
 HW1=1
 HW2=1
   N=7
 C12=6
H12A=1
.
.
.
.

Could the above mentioned error may be due to a bug in gmx density?

Thank you in advance.


-- 
Best Regards,
Ganesh Shahane