On 6/6/12 11:07 AM, Bao Kai wrote:
HI, all,
I want to use MTTK for the pressure coupling for NPT simulation, while
I can not get the correct pressure value.
The following result is a simulation with 1000 SPC-E water molecules
with temperature 303.15K and pressure 1 bar.
Statistics over 1000001 steps [ 0.0000 through 1000.0000 ps ], 3 data sets
All statistics are over 200001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 303.155 0.016 5.54033 0.0532334 (K)
Pressure 138.295 1.3 429.699 -5.68756 (bar)
Density 1002.82 0.24 8.04912 0.668867 (kg/m^3)
.
The following is the mdp file
title = fizzy water
; Run parameters
integrator = md-vv ; velocity-verlet integrator
nsteps = 1000000; 0.001 * 1000000 = 1000 ps, 1 ns
dt = 0.001 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps. Incr by *10
nstvout = 1000 ; save velocities every 2 ps. Incr by *10
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps. Incr by *10
nstenergy = 1000 ; save energies every 2 ps. Incr by *10
nstlog = 1000 ; update log file every 2 ps. Incr by *10
; Bond parameters
continuation = yes ;<-- Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = nose-hoover ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 303.15 ; reference temperature, one for each group, in K
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; turning on pressure coupling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;<-- Pressure coupling is on
pcoupl = mttk; Pressure coupling on in NPT
nstpcouple = 1;
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ;<-- Velocity generation is off
;
Could anybody tell me anything wrong with my configuration?
Probably nothing. Pressure is a very hard term to converge, as noted here:
http://www.gromacs.org/Documentation/Terminology/Pressure
Note that the manual warns that you will get very large oscillations in the
pressure value if you don't start from a reasonable (i.e., previously
equilibrated) value. Using Berendsen for initial NPT equilibration is more
common and more stable.
Your simulations are also very short. Pressure (and other terms) may require
more than just 1 ns to converge, but you should also bear in mind that the value
you obtained is 138.295 ± 429.699. Is that significantly different from the
target value? Given the magnitude of the standard deviation, I would say no.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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
