[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.

Catch ya,

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
a nail.

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