Hi,<br><br>I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :-<br>genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro <br><br><br>The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :-<br>
<br><br>Reading solute configuration<br>GRoups of Organic Molecules in ACtion for Science<br>Containing 3620 atoms in 231 residues<br>Initialising van der waals distances...<br><br>WARNING: masses and atomic (Van der Waals) radii will be determined<br>
based on residue and atom names. These numbers can deviate<br> from the correct mass and radius of the atom type.<br><br>Reading solvent configuration<br>"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"<br>
solvent configuration contains 648 atoms in 216 residues<br><br>Initialising van der waals distances...<br>Will generate new solvent configuration of 46x46x46 boxes<br>Generating configuration<br>Sorting configuration<br>
Found 1 molecule type:<br> SOL ( 3 atoms): 21024576 residues<br>Calculating Overlap...<br>box_margin = 0.315<br>Removed 1047843 atoms that were outside the box<br><br clear="all">What have gone wrong for solvation to take this much time on 12 processors CPU.<br>
-- <br>Bharat<br><br>