[gmx-users] Density Differences

[Justin A. Lemkul]

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
> 

-- 
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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

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