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
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.
genbox is not parallelized; you can only use 1 CPU.
You've added 21 million water molecules (yikes!) to the box and genbox is trying
to remove over 1 million atoms - I'd say your box is much too large for a solute
of 3620 atoms, by several orders of magnitude. You're probably running out of
memory to do this operation.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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