On 2/12/2011 12:37 PM, bharat gupta wrote:
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
This is 21 million water molecules, from far too many boxes for a 3K
atom protein. A few tens of thousands of water molecules would be
normal. Something is wrong with the coordinates or box dimensions of
your -cp file.
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.
All water atoms have to be tested for overlap with all protein atoms -
that's expensive. Also, no GROMACS tools apart from mdrun actually use
more than one processor of those available.
Mark
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