[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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