[gmx-users] Reg; MD of DCE part II
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Tue Oct 26 13:28:15 CEST 2010
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.
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> 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>> 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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