[gmx-users] Re: Protein ligand simulation

[Justin A. Lemkul]

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

-- 
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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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