[gmx-users] Large number of solvent molecules

[Dallas Warren]

>From the box volume printed in the script output it appears you have a box that is approximately a 28nm cube.  And that size box requires a significant number of water molecules to fill up, so that number you have in there (~770,000) seems about correct.

If you want to have less water molecules, then you will need to make the simulation cell smaller.  Whether that is possible or not depends on what you are looking to observe, how big the molecule you are solvating is etc.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Nikunj Maheshwari
> Sent: Tuesday, 14 May 2013 3:04 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Large number of solvent molecules
> 
> Dear all,
> 
> I am trying to see the folding of a 89 aa peptide. So I am setting up
> the
> system from linear conformation.
> I gave the following commands to build the box and add the solvent
> molecules.
> 
> editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
> 
> genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro
> 
> Reading solute configuration
> Go Rough, Oppose Many Angry Chinese Serial killers
> Containing 1440 atoms in 89 residues
> Initialising van der waals distances...
> 
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>          based on residue and atom names, since they could not be
>          definitively assigned from the information in your input
>          files. These guessed numbers might deviate from the mass
>          and radius of the atom type. Please check the output
>          files if necessary.
> 
> 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 18x18x13 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
>     SOL (   3 atoms): 909792 residues
> Calculating Overlap...
> box_margin = 0.315
> Removed 324522 atoms that were outside the box
> Neighborsearching with a cut-off of 0.48
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
> System total charge: 0.000
> Grid: 73 x 73 x 51 cells
> Successfully made neighbourlist
> nri = 3007232, nrj = 82473964
> Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653
> atoms.
> Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182
> atoms.
> Added 776673 molecules
> Generated solvent containing 2330019 atoms in 776673 residues
> Writing generated configuration to outh2o.gro
> 
> Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1#
> Go Rough, Oppose Many Angry Chinese Serial killers
> 
> Output configuration contains 2331459 atoms in 776762 residues
> Volume                 :     23276.3 (nm^3)
> Density                :     1001.32 (g/l)
> Number of SOL molecules:  776673
> 
> Processing topology
> Adding line for 776673 solvent molecules to topology file (topol.top)
> 
> 
> Later on, I used -d 0.5. I still get around 710000 water molecules in
> the
> system.
> 
> Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9
> A
> and 8.4 A respectively.
> 
> I need to know if I have done something wrong in setting up the system.
> Is
> there any way to get feasible number of solvent molecules?
> 
> Thanks....
> Nikunj
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