[gmx-users] g_spatial: merging solvent ond solute:::need some distance

Christopher Neale chris.neale at alum.utoronto.ca
Fri Dec 27 06:26:45 CET 2013

To help you, I need to see the exact commands that you used. Best is if you can put it all in a script, run the script to be sure that you see the problem, and then copy and paste the script back to this list. Failing that, copy and paste your commands and tell me what your command-line input was to each tool.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of srinivasa rao lanke <srinu1982 at hotmail.com>
Sent: 26 December 2013 11:12
To: gmx-users at gromacs.org
Subject: [gmx-users] g_spatial: merging solvent ond solute:::need some  distance


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 simulated one molecule with water system
1 step i selected solute i.e molecule and totatel system
2 step also same like 1st step
3 step i selected four atoms from molecule and water OW
grid.cube file created and seen in VMD

I am looking for sdf of molecule group and water Oxygen

I am seeing sdf surface and my molecule atoms are overlapping in 3D view

but most of the publication i have seen that there is a distance between sdf
surface and
water oxygen.

Could you please suggest me how to correct this problem.

thank you very much advance

phd student
IIT hyderabad

View this message in context: http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list