[gmx-users] RE: ask about SDF

Dallas Warren Dallas.Warren at monash.edu
Mon Apr 30 01:25:05 CEST 2012

I have sent this email to the gromacs users emailing list.

I don't actually use g_spatial as it doesn't do what I want it to, I use the older g_sdf script.  So can't comment on the output or really help you with it.

What you are doing seems right from a quick look through.  From what you have told the script to so, it seems like it has done exactly what you asked it to.  But without seeing what the system looks like, how it behaves etc, can't say anything beyond that.

When I don't see what I expect, I start with a very simple example, ensure that I what I expect there, then make things gradually more complex.  That way you can work out if you are using the script incorrectly or what you expected to see is actually incorrect.

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.

From: Ianatul Khoiroh [mailto:ianatul_khoiroh at yahoo.com]
Sent: Friday, 27 April 2012 6:14 PM
To: Dallas Warren
Subject: ask about SDF

Dear Dr. Dallas Warren,

I am sorry for sending you a personal e-mail. FYI, I got your email address from gmx-user mailing list.

I am new to Gromacs and I did little stuff already in it for the last two months.  Briefly, my system consist of 10 oligomers + 990 of solvents in cubic box.  I did 15 ns NPT equilibration and currently I am doing analysis stuff such as RDF, density, viscosity, etc. And now I want to try using g_spatial but I stuck on it. I would like to know if you can help me in this.

In Gromacs 4.5.4 manual, they wrote like this:

1. Use make_ndx to create a group containing the atoms around which you want the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface

I have tried to follow those steps but I coud not get any pretty SDF picture like those I read in many papers. :D
This is what I have done following the above mentioned steps:
step 1: I have my index file
step 2: I choose my oligomers ("solute", 10 oligomers) as group for centering and I select "system" (10 oligomers + 990 solvents) as an output group
step 3: Again, I choose "solute" and choose "system" as an output
step 4: I run g_spatial and select "990 solvents" for both calculation and output. It gives me warning to increase nab values, so I increase the nab = 100. I got grid.cube but the size of the file is not that big (the manual says it is around 3 copies of *.xtc file).
step 5: I load grid.cube into VMD as an isosurface. I got only a sphere of solvents there on the VMD display

I would like to know if you could tell me what principally have I did wrong here.... I run Gromacs 4.5.5 in Cygwin.

I really appreciate your help......Thank you very much.


Ianatul Khoiroh
Thermophysical Properties Lab. E2-504
Dept. of Chemical Engineering
National Taiwan University of Science and Technology (NTUST)
#43 Keelung Road, Sec. 4, Taipei 106, Taiwan R.O.C
Phone: +886-2-2733-3141 #7605
E-mail: ianatul_khoiroh at yahoo.com<mailto:ianatul_khoiroh at yahoo.com>

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