[gmx-users] Reg; MD of DCE part II

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
> Hi Dallas / all
> 
> I looked up at the pressure coupling section and i found how to keep the 
> box size same for two axis and change only one axis (i used 
> semiisotropic pressure coupling type) but when i did that the average 
> pressure i get after the run is negative where as i want it be close to 
> 1 bar?. i dont know what might have gone wrong.
> 
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Pressure (bar)             -661.673    675.593    674.292  -0.725677   
> -145.136
> 
> similary when i give g_energy -f npt.edr -o density.xvg the density 
> option is not there to select it interactively. hence i am not able to 
> plot the density graph.why?
> 

All of the above suggests you've gotten your files confused and you're analyzing 
an .edr file from an NVT run, not NPT.  If indeed you did NPT, the density term 
would appear below, along with "Volume."  The only time when these terms are not 
written is if the volume of the unit cell is static (i.e., NVT).


> 1  Bond             2  Angle            3  Ryckaert-Bell.   4  
> LJ-14        
> 5  Coulomb-14       6  LJ-(SR)          7  Disper.-corr.    8  
> Coulomb-(SR) 
> 9  Coul.-recip.    10  Potential       11  Kinetic-En.     12  
> Total-Energy 
> 13  Conserved-En.   14  Temperature     15  Pressure-(bar)  16  
> Vir-XX       
> 17  Vir-XY          18  Vir-XZ          19  Vir-YX          20  
> Vir-YY       
> 21  Vir-YZ          22  Vir-ZX          23  Vir-ZY          24  
> Vir-ZZ       
> 25  Pres-XX-(bar)   26  Pres-XY-(bar)   27  Pres-XZ-(bar)   28  
> Pres-YX-(bar)
> 29  Pres-YY-(bar)   30  Pres-YZ-(bar)   31  Pres-ZX-(bar)   32  
> Pres-ZY-(bar)
> 33  Pres-ZZ-(bar)   34  #Surf*SurfTen   35  Mu-X            36  
> Mu-Y         
> 37  Mu-Z            38  T-System        39  Lamb-System
> 
>  and i have given my mdp file below. any help is highly appreciated.
> 
> title        = DCE NPT equilibration
> integrator    = md       
> nsteps        = 200000
> dt        = 0.001      
> nstxout        = 1000      
> nstvout        = 1000       
> nstenergy    = 1000       
> nstlog        = 1000       
> constraint_algorithm = lincs  
> constraints    = all-bonds   
> lincs_iter    = 1      
> lincs_order    = 4    
> ns_type        = grid   
> nstlist        = 5  
> rlist        = 1.0      
> rcoulomb    = 1.0  
> rvdw        = 1.0   
> coulombtype    = PME  
> pme_order    = 4      
> fourierspacing    = 0.16   
> tcoupl        = V-rescale  
> tc-grps        = system  
> tau_t        = 0.1    
> ref_t        = 300        
> pcoupl        = Parrinello-Rahman 
> pcoupltype    = semiisotropic  
> tau_p        = 2.0 2.0    
> ref_p        = 1.0 1.0       
> compressibility = 0.0 4.5e-5

For what its worth, if this is your initial equilibration, using 
Parrinello-Rahman coupling may not be your best choice.  If your system is far 
from equilibrated, the P-R method (in my experience) can allow for wide 
oscillations, and ultimately system instability.  Nothing wrong with Berendsen 
for your initial equilibration.

But again, if pressure coupling was actually used, you'd have Volume and Density 
terms in the .edr file, along with a more sensible value of pressure.

-Justin

> pbc        = xyz  
> DispCorr    = EnerPres   
> gen_vel        = no    
> 
> Regards
> Vinoth
> 
> 
> On Tue, Oct 26, 2010 at 5:33 AM, Dallas Warren <Dallas.Warren at monash.edu 
> <mailto:Dallas.Warren at monash.edu>> wrote:
> 
>      >I performed md simulation of 108 dichloroethane molecules in
>     isothermal-isobaric ensemble with the box size
> 
>      >3.002*2.17*2.17. after the simulation my box size has changed
>     considerably from the initial size to 2.87882 2.08095
> 
>      >2.08095.why this happens?
> 
>      
> 
>     Density was obviously too lower under the conditions of the
>     simulation.  Look at the change of pressure, volume and density for
>     the box during that simulation.
> 
>      
> 
>      >my second question is can i have a control over the box dimensions
>     changes during md (i.e when the box dimensions
> 
>      >changes during md i want to change it only on one axis(say x
>     axis) and want to keep the length of the other two axis (say
> 
>      >y and z) same as that of my initial box size? any help is highly
>     apprecited.
> 
>      
> 
>     Look at the pressure coupling settings, look at anisotropic pressure
>     coupling.
> 
>      
> 
>     Catch ya,
> 
>     Dr. Dallas Warren
> 
>     Medicinal Chemistry and Drug Action
> 
>     Monash Institute of Pharmaceutical Sciences, Monash University
>     381 Royal Parade, Parkville VIC 3010
>     dallas.warren at monash.edu <mailto: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.
> 
>      
> 
>      
> 
> 
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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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