Sai Pooja wrote:
Reply inline...
On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Sai Pooja wrote:
Hi,
I have a system of 3600 LJ particles in a plane (using
freeze-dimension option in z). I am running npt runs using
Semi-isotropic pressure coupling with Parrinello-Rahman
barostat. I have a few concerns:
1) On the gromacs website, a webpage mentions that this type of
pressure coupling may not be accurate
Please provide a link when making this kind of statement.
http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman
<http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman>
Bugzilla entry 14 is ancient, and has long since been resolved:
http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues
2) It takes a really long time for the system to reach the
reference pressure > 500ns. Particularly the Pxx, Pyy terms are
very different and take an extremely long time to converge to a
common value.
integrator = md
dt = 0.001
nsteps = 50000000
; OUTPUT CONTROL OPTIONS
nstxout = 0 ; No output, except for last frame
(coordinates)
nstvout = 0 ; No output, except for last frame
(velocities)
nstfout = 0 ; No output, except for last frame
(forces)
nstlog = 1000000 ; Write every nth step to the log
nstenergy = 1000000 ; Write energies at every n step
nstxtcout = 1000000 ; Do not write a compressed tr
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Cut-off
rcoulomb = 1.1225
vdw-type = User
rvdw = 1.1225
table-extension = 0
; Temperature coupling
tcoupl = nose-hoover
tc-grps = ARAR
tau_t = 0.1
ref_t = 120.2717
; Pressure coupling
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau-p = 1.0 1.0
compressibility = 1e-5 0 ;Dont know
ref-p = 69 0
;Generate velocities for startup run
gen_vel =no
gen_temp =120.2717
gen_seed =-1
;Non equilibrium MD steps
freezegrps =ARAR
freezedim =N N Y
;Constraints
constraints = all-bonds
constraint_algorithm = Lincs
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 90
;unconstrained_start = no
;shake_tol = 0.0001
Do you run any equilibration prior to applying these parameters? Both N-H and
P-R allow for wide fluctuations in temperature and pressure, respectively, which
are exacerbated by systems that are not sufficiently equilibrated. Hence it
could take a very long time if you do not equilibrate well using, i.e. a weak
coupling scheme first.
-Justin
What was your equilibration protocol? What are your .mdp settings?
-Justin
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
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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--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
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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