[gmx-users] Large number of solvent molecules

[Erik Marklund]

Hi,

Have a look at the following article. It describes a non-standard box type that seems ideal for your application. I don't know what is the latest gromacs version where it is implemented, however.

Author = {Wassenaar, TA and Mark, AE},
Title = {{The effect of box shape on the dynamic properties of proteins simulated
   under periodic boundary conditions}},
Journal = {{JOURNAL OF COMPUTATIONAL CHEMISTRY}},
Year = {{2006}},
Volume = {{27}},
Number = {{3}},
Pages = {{316-325}},


On 14 May 2013, at 07:44, Nikunj Maheshwari <nixcrazyforher at gmail.com> wrote:

> 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
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists