[gmx-users] Reg; MD of DCE part II
Dallas Warren
Dallas.Warren at monash.edu
Tue Oct 26 23:46:02 CEST 2010
And also graph the pressure with time, you will see that it is probably
fluctuating wildly, so deviations from such a small number as 1 in this
context is not surprising.
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.
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Tuesday, 26 October 2010 10:31 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] Reg; MD of DCE part II
>
>
>
> vinothkumar mohanakrishnan wrote:
> > Hi Justin
> >
> > Thank you very much for your comments. I actually found that after
> > posting the question. sorry I have a new question i did NPT
> > equilibration of DCE molecules and the average pressure turns out to
> be
> > 3.4726 (bar) where as i want the pressure it to be 1 bar. what
> further i
> > need to do?.below is what i got from the g_energy command.
> >
>
> Do more equilibration. Clearly your system is not equilibrated if it
> has not
> reached the desired equilibrium conditions.
>
> -Justin
>
> > Energy Average RMSD Fluct. Drift
> > Tot-Drift
> >
---------------------------------------------------------------------
> ----------
> > Pressure (bar) 3.47263 767.297 765.878 0.8078
> > 161.561
> >
> > below is my mdp file any help is highly appreciated
> >
> > title = DCE NVT equilibration
> > cpp = usr/bin/cpp
> > integrator = md
> > nsteps = 200000
> > dt = 0.001
> > nstxout = 1000
> > nstvout = 1000
> > nstenergy = 1000
> > nstlog = 1000
> > constraint_algorithm = shake
> > constraints = none
> > unconstrained_start = yes
> > shake_tol = 0.0001
> > morse = no
> > ns_type = grid
> > nstlist = 5
> > rlist = 1.0
> > coulombtype = PME
> > rcoulomb = 1.0
> > vdwtype = Cut-off
> > rvdw = 1.0
> > pme_order = 4
> > fourierspacing = 0.16
> > pbc = xyz
> > 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
> > DispCorr = Enerpres
> > gen_vel = yes
> > gen_temp = 300
> > gen_seed = 173529
> >
> > Regards
> > Vinoth
> >
> >
> >
> > On Tue, Oct 26, 2010 at 4:34 PM, Justin A. Lemkul <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > 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>
> > <mailto: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>
> > <mailto: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 <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
>
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