[gmx-users] Reg; MD of DCE part II
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 26 13:30:32 CEST 2010
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.
>
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list