[gmx-users] electron density maps

kia balali kiabalali50 at hotmail.com
Mon Oct 7 18:14:28 CEST 2002

Dear All,

I have been creating an electron density map for my explicit bilayer models. 
I decided on creating a "template" which involves a group specific 
electrons.dat file &  a specific *.ndx file made using the make_ndx command. 
My groups are done using the experimental model by Wiener & White 
(originally devised for DOPC)which divides them up into 8 groups.

As I understand it, make_ndx is only interested in the structure file (*.gro 
or PDB) and not the trajectory (*.xtc or *.trr), seeing as my ensemble is 
NPT....then theoretically it shouldn't matter if I create templates  and use 
them when I run g_density using different trajectory files & topol.tprs from 
my various MD runs whilst using the -ed option to calculate electron 

Seems reasonably straightforward, i'm just a bit worried I may have missed 
something seeing as i'm planning to publish this work ....and it's also part 
of my PhD .....

will be most grateful if the likes of Drs. Lindahl or Van Der Spoel can give 
me their thoughts ;-)

Groeten (Best wishes)


Kia Balali-Mood
Dept. of preclinical Veterinary Sciences
Laboratory of Membrane Biophysics
The Vet School
College of Medicine & Veterinary Medicine
University of Edinburgh

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