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

srinivasa rao lanke srinu1982 at hotmail.com
Thu Dec 26 17:12:57 CET 2013


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 

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