[gmx-users] g_spatial Problem

[Christopher Neale]

Can you please describe the system a bit more (especially how many molecules of each of the 4 types you have) and also provide more information about what you want to obtain (sdf, obviously, but of what and ideally also why).

1. your procedure could be ok, but also maybe not. Depends on what you are trying to achieve. I am presuming there is only 1 "anion" though (based on the image you sent me off-list) although that doesn't jive with your question #2, so I am confused here. Fitting over multiple "anion" molecules that are separately diffusing is not likely what you want.... -- (B) the grid.cube file is a rectangular matrix, so that is expected. The regions with non-zero density will not fill up the entire rectangle though, usually.

2. The g_spatial program is intended for a single central fitting group. There was an old program called g_sdf that may (or may not) do what you want -- it was intended to look at multiple central solutes though as I recall. If you want to have the cumulative sdf over all "anions" then you have to do more processing. What I do in this case is this. Say I have 10 "anion" solute molecules (the central group for which you want to build an sdf of other molecules around ... I'm going to call this the solute from here on). Then you make 10 copies of the trajectory in which you only output one solute (different one each time) and also include all the solvent (this part will be the same in all trajectories). Then concatenate all of these trajectories with trjconv -cat -nosort. You may need to create a .tpr for this trajectory, or possibly g_spatial will accept a .gro or .pdb as input to the -s option. Now you take this concatenated trajectory and run it through all the steps that you listed in your email. This should give you what you want.

Note: if your solute is flexible, then you may not want to fit on the entire solute. That may lead to smearing. I would certainly try it, but I would also try fitting on different subsets of the solute (like one charged region) that have at least 3 atoms and make that sdf as well.

Good luck.
Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Rubaiyet Abedin <abedin.r at husky.neu.edu>
Sent: 26 September 2016 13:18:46
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] g_spatial Problem

Dear Sir,

Hope you are doing good. I am working with a system that contains ionic
liquid and refrigerant. To avoid complication let’s say my system contains
the following:

Cation (1)

Anion (2)

Type A (3)

Type B (4)



And the system (0). I want to get the spatial distribution function of type
A around Anion. So the central molecule will be the anion. I used the
following commands:



*1.      **make_ndx -f bath_298K.part0001.gro -o bath_298K_index.ndx*



*2.      **trjconv -s bath_298K.tpr -f bath_298K.part0001.xtc -o
bath_298K_b.xtc -center  -ur compact -pbc none  -n bath_298K_index.ndx*



I selected Anion (2) for centering and system (0) for output



*3.      **trjconv -s bath_298K.tpr -f bath_298K_b.xtc -o bath_298K_c.xtc
-fit rot+trans*



I selected Anion (2) for fitting and system (0) for output



*4.      **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and type A (3) to output coordinates



*5.      **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and Anion (2) to output coordinates



I got two grid.cube file and load them into vmd. For the grid.cube (from
step 4) I chose the isosurface value 0.01 and viewed the other cube file as
a single molecule. I have several question:



1.      Do you think I am following the right procedure specially I am
confused and step 4 and 5. After loading both of the grid.cube file I got
something like this the attached.

 For some cases I even got rectangular box. Should it be a sphere?

2.      I am choosing a random Anion (2). Every time I choose a different
anion, I see different cloud shape. I am confused if I am doing something
wrong or I have to choose the central molecule following any specific
technique.


Please help me out with this. Thanks a lot.



Rubaiyet