[gmx-users] Large number of solvent molecules

XAvier Periole x.periole at rug.nl
Tue May 14 09:53:25 CEST 2013 

Well, a linear 80aa peptide will need that much water anyways! 

The question is more how relevant and realistic is such a structure and how long the peptide is going to keep it? You could resolvate it after some time, reducing the box, you could also start by a vacuo simulation to help colapse your peptide. 

But the chance to actually observe folding of such a peptide from a single MD simulation is about zero. Even using enhance sampling the chance is about zero unless you get some large access to supercomputers. See DE Shaw papers on folding. 

On May 14, 2013, at 9:44, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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
> 
> -- 
> 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

More information about the gromacs.org_gmx-users mailing list