[gmx-users] g_sdf again

syma syma.khalid at bioch.ox.ac.uk
Fri Mar 30 12:39:07 CEST 2007



Thanks for your help with this.


The problem was that the size of my 3d grid was too small (I was just using
the default 1x1x1 nm). I have now used a grid size that matches my system
and have a sensible gro file.


Best wishes,





From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Qiao Baofu
Sent: 30 March 2007 08:19
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sdf again



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


> 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 

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
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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