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

vinothkumar mohanakrishnan kmvinoth at gmail.com
Tue Oct 26 10:22:29 CEST 2010


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?

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
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>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
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
>
>
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