[gmx-users] g_sdf -> and g_spatial

Dallas Warren Dallas.Warren at monash.edu
Wed Mar 7 01:21:26 CET 2012

I know, bit of a zombie topic (May 2011) to be digging out of the archives here.

I have previously used g_sdf rather extensively and needed to generate some spatial distribution functions for a paper.  Started to looked into g_spatial to see if that can do what I want it to, since g_sdf has been removed from the distribution.  g_spatial is not what I expected and seems to me to be actually less flexible than g_sdf was, though I are more than likely wanting to use it slightly differently way to the person that wrote/developed it.  g_spatial requires a single solute molecule that is relatively stationary and centered for the length of the trajectory (which needs some running through trjconv to get this done), then it calculates the SDF relative to this molecule.  g_sdf makes no such assumption and you can have many molecules which you can then calculate and get the average SDF.

Is there the possibility that we can either have g_sdf added back into the distribution (or is there documentation / discussion somewhere that I can read to see why it was removed), or the functionality that has been lost added into g_spatial (probably not trivial)?  Don't like my chances though ;-), but can't hurt to ask.

I am currently using a 4.0.7 installation of GROMACS, which includes g_sdf, to generate the appropriate images I need.

> Justin Lemkul wrote:
> Nilesh Dhumal wrote:
> > Hello,
> > 
> > I have a system with glucose + ionic liquids (cation + anion).
> > 
> > I am trying calculate distribution of cation and anion around glucose
> > molecule using g_sdf. I want to plot distribution of cation and anion is
> > same figure. I run the following command
> > 
> > g_sdf -f 3.trr -s 3.tpr -n glu-emi-dmp-128-no.ndx -mode 2 -o -r
> >
> > I selected two atoms from glucose and 3rd and 4th groups are cation and
> > anion respectively.
> > 
> > All the coordinates in  refmol.gro are zero.
> > 
> > I am using gromacs version 4.0.7.
> > 
> > Why all the coordinates in  refmol.gro are zero.
> > 
> g_sdf is relatively inflexible; it was designed (it appears) around calculations 
> involving water.  g_spatial is much more flexible, and I believe it was for this 
> reason that g_sdf has been removed from newer Gromacs versions.  Try g_spatial 
> instead.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 

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