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 questions: 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 file I got something like this: 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
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