Hi ,
I have a protein in a mixed solvent simulations. My probes are ethanol, acetontrile, imidazole and pyrimidine.
grid command does the per atom binning of atomic densities. However, if I want to perform the center of mass binning rather than the per atom binning, how to modify the code. In simple words " I want to bin the center of mass of molecules rather than bin each atom. Any help will be appreciated. Daniel proposed a way to do this but it is probably not working. Thanks

A sample grid command I use
parm 3kfa_layer_ACN_H2O_5-95vv.prmtop
trajin production.1.crd 1 1250 1
autoimage
#Align trajectory to reference structure by minimizing RMSD
reference /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/setup_solvbox/3kfa_layer_ACN_H2O_5-95vv.pdb
strip :Cl-,Na+
rms reference mass out 3kfa_ACN_10-15ns_md_CA_rmsd.txt :1-286@CA
#Write out grid count of probe occupancy
grid out 3kfa_ACN_10-15ns_C3N_center.xplor 200 0.5 200 0.5 200 0.5 :C3N origin max 0.9
grid out 3kfa_ACN_10-15ns_WAT.xplor 200 0.5 200 0.5 200 0.5 :WAT origin max 0.9

grid out [email protected] 200 0.5 200 0.5 200 0.5 :C3N@C3 origin max 0.9
grid out [email protected] 200 0.5 200 0.5 200 0.5 :C3N@C2 origin max 0.9
grid out [email protected] 200 0.5 200 0.5 200 0.5 :C3N@N1 origin max 0.9
#Correct for systematic error induced by ptraj grid function
translate x -0.25 y -0.25 z -0.25