[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:
>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)
>Dept. of preclinical Veterinary Sciences
>Laboratory of Membrane Biophysics
>The Vet School
>College of Medicine & Veterinary Medicine
>University of Edinburgh
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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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