> my molecule ha 121 residues the rest is water which makes the whole system 5073
> residues, i.e 17100 atoms.
> My solvent mask should be 14756 atoms (water), but below ptraj says: " Solvent
> atom selection is :1.N76,:122-5073" because solvent is just 122-5073!
As mentioned, you need to read up on the syntax of atom selection; solvent
should be 14856 atoms... You have selected that and also :1.N76
> my other question, you mentioned in your email "distance RDF-value integral"
> what is this please?
> ________________
> trajin pdb_bond_wat_md1_exp.mdcrd
> trajin pdb_bond_wat_md2_exp.mdcrd
> center :1-5073 origin mass
> image origin center familiar
> radial pdb_bond_wat_rad_dens.rdf 0.5 10.0 :WAT:1.N76 density 0.033456
You likely just want to center the solute, :1-121, not the entire box,
prior to imaging.
center :1-121 mass origin
> PTRAJ: radial pdb_bond_wat_rad_dens.rdf 0.5 10.0 :WAT:1.N76 density 0.033456
> Mask [:WAT:1.N76] represents 14857 atoms
> [No output trajectory specified (trajout)]
Yep, (5073 - 121)*3 + 1 extra atom selected... It is so slow since it is
doing the PMF of every atom to every atom (in your selection).
Add a space between selections; also you likely do not want the RDF to
water but separate RDF's of water oxygen's or hydrogens...
radial out 0.5 10.0 :WAT.O :1.N76
--tec3
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Received on Tue Jul 27 2010 - 09:00:04 PDT
