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 <jalem...@vt.edu
<mailto:jalem...@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.war...@monash.edu <mailto:dallas.war...@monash.edu>
<mailto:dallas.war...@monash.edu
<mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@monash.edu>
<mailto:dallas.war...@monash.edu <mailto:dallas.war...@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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