[gmx-users] g_sdf again
Dallas B. Warren
Dallas.Warren at vcp.monash.edu.au
Thu Mar 29 23:51:17 CEST 2007
> I am using g_sdf to calculating the spatial distribution of
> lipid headgroups around other species in my system.
> The thing is when I get the gro file (produced by using the -r flag in
> g_sdf) and then look at this in vmd or chimera with my
> spatial density file (plt), the reference gro file is not
> positioned 'in' the box of density produced by g_sdf.
> Is this as it should be and I am interpreting my results
> incorrectly, or have I set up my coordinate system incorrectly?
That does sound a bit unusual.
However, I use g_sdf quite extensively but don't use the reference
structure function. Reason for this, is I have found that the one
generated for the molecules I simulate it is highly distorted and the
corresponding atom locations do not match up with where they they are
located if you calculate the sdf for the non-coordinate atoms within the
molecule. So I use a representative molecule, rotate to match the sdf
for atoms within the molecule, then use that. Not the best way to do
it, but it gets what I need.
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
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