[gmx-users] Re: Protein ligand simulation

[bharat gupta]

Hi,

I am trying the simulation of a docked complex of my protein . While
solvating the box using the following command :-
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro


The processing does not stop and continues to run . Here's the output that
I got while solvating the box , which is still continuing :-


Reading solute configuration
GRoups of Organic Molecules in ACtion for Science
Containing 3620 atoms in 231 residues
Initialising van der waals distances...

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 46x46x46 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 21024576 residues
Calculating Overlap...
box_margin = 0.315
Removed 1047843 atoms that were outside the box

What have gone wrong for solvation to take this much time on 12 processors
CPU.
-- 
Bharat
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