[gmx-users] Large number of solvent molecules

[Nikunj Maheshwari]

Thank you Dr. Dallas. Yes I think the issue is that the starting
conformation is linear, as I want to study its folding properties. I tried
the same with helical starting conformation, and got around 110000 water
molecules, which is still ok.
I am trying to find a way to simulate a 89 aa peptide in linear starting
conformation such that the simulation is practically feasible.

On Tue, May 14, 2013 at 10:45 AM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

> >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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