[gmx-users] Density Differences

[Justin A. Lemkul]

Kavyashree M wrote:
> I am sorry I did not include it in the mail: i used the following:
> 
> pcoupl                  = Parrinello_Rahman    
> pcoupltype              = isotropic            
> tau_p                   = 2.0                  
> compressibility         = 4.5e-5        
> ref_p                   = 1.0                  
> 
> I agree that density of water is different  depending on the model used,
> so for tip4p water what is the range of fluctuations accepted? So that
> we can conclude that the difference is not due to any other reason but
> the water model used.
> 

The extent of fluctuation in any pressure-related term depends on the size of 
your system and several of the .mdp settings.

http://www.gromacs.org/Documentation/Terminology/Pressure

For the actual target value of TIP4P density, refer to the literature.  The 
TIP4P citation is provided in the Gromacs manual.

-Justin

> Thanking you
> With regards
> Kavya
> 
> On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Kavyashree M wrote:
> 
>         Dear gromacs users,
>          I am trying to simulate a 225aa protein at 300K in water,
>         with OPLSAA force filed, tip4p water model, using the
>         parameters below (for pressure equilibration) during
> 
> 
>     You're not doing NPT.  You haven't specified pcoupl or any of the
>     other relevant parameters, so you're doing NVT.
> 
> 
>         position restrained md.
> 
>         integrator              = md                  dt                
>              = 0.002                nsteps                  = 50000    
>               nstcomm                 = 10               nstlist        
>                 = 5                  ns_type                 = grid    
>               pbc                     = xyz             rlist          
>                 = 1.40
>         coulombtype             = PME  rcoulomb                = 1.40  
>           vdwtype                 = Switch           rvdw_switch        
>             = 0.9              rvdw                    = 1.00          
>               fourierspacing          = 0.12              pme_order    
>                   = 4                  ewald_rtol              = 1e-5  
>                     optimize_fft            = yes Tcoupl                
>          = nose-hoover       tc_grps                 = Protein  Non-Protein
>         tau_t                   = 0.4      0.4         ref_t            
>               = 300      300        nh-chain-length         = 1    
>         gen_vel                 = no     continuation            = yes  
>         constraints             = all-bonds
>         constraint-algorithm    = LINCS
>         lincs-order             = 4            lincs-iter              =
>         1               lincs-warnangle         = 30
>         when I calculate the densities, the average came out to be
>         1025.91 kg/m^3,
>         Could anyone please clarify me the reason for this density.
> 
> 
>     Simulating with the right ensemble (NPT) will equilibrate the
>     pressure and thus density.  As a fundamental point, please also
>     realize that each water model has its own (different) expected
>     density value, which is also influenced somewhat by the remaining
>     contents of the system.  Therefore, the result you obtain may not be
>     in exact agreement with experimental bulk density of water.
> 
>     -Justin
> 
> 
>         Thanking you
>         With regards
>         Kavya
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================