[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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