[gmx-users] electron density maps

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 7 18:32:04 CEST 2002

On Mon, 7 Oct 2002, kia balali wrote:

>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 ;-)
Here we go:
if you want realistic electron density maps, I'd suggest you try to use
some CCP4 programs from a structure file. Otherwise, I don't know what you
mean (I just assume it is not density profiles which g_density produces)

>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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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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