[gmx-users] g_sdf again

Qiao Baofu qiaobf at gmail.com
Fri Mar 30 09:18:51 CEST 2007

2007/3/29, Dallas B. Warren <Dallas.Warren at vcp.monash.edu.au>:
> Syma,
> > 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.

Yes. I also found that.
Because  I want to use the COM of the reference group to calculate the sdf,
and the problem of "-r" flag, I rewrite this program. It works. But it seems
my program always uses too much memory. Who can give some suggestions to
save the memory?  Thanks a lot!

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
> Lecturer
> 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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Sincerely yours,
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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