[gmx-users] Large number of solvent molecules

Nikunj Maheshwari nixcrazyforher at gmail.com
Tue May 14 07:03:40 CEST 2013

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

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
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

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?


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