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>> 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>
+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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists