Dear GROMACS users,
I am new to GROMACS, and recently started using the version 4.6.5.
I have seen a lot of NPT related issues raised earlier in this forum, but in
my case the error looks much more severe.
I am following Justin Lemkul's tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/01_genconf.html)
on Biphasic system, containing cyclohexane and water.Everything went well
till the NPT simulation to bring system to reference pressure of 1 bar.
Here are the details of the system , .mdp file , what I did and where I
find the problem.
SYSTEM : 512 cyclohexane + 2720 water molecules.
CURRENT STATUS:
(1) Energy minimization : energy converged.
(2) NVT (tcoupl=berendsen , tau_t=0.1ps / ref_t=298K)
completed and target pressure of 298 K attained.
(3) NPT (tcoupl=nose-hoover, tau_t=0.5ps / pcoupl=berendsen,
tau_p=1ps / ref_p = 1bar , total time=15 ns) completed with the following
result:
Energy Average Err.Est. RMSD
Tot-Drift
-------------------------------------------------------------------------------
Pressure 1.08924 0.67 114.66
-1.74033 (bar)
Since berendsen barostat doesn't generate the true ensemble, an
equilibration with pcoupl=parrinello-rahman is performed in the next step.
(4) NPT (pcoupl=parrinello-rahman, tau_p=5ps, total time=5ns)
----> PROBLEM FACED: The average pressure too high as shown below which I
feel is not going to improve.
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 23.6651 0.53 144.464 -1.00634 (bar)
I am aware of the fact that pressure is subject to large fluctuations in
small sized systems and that this may affect the average value of the
pressure. But , here the average pressure looks too large to be ignored. The
pressure-vs-time graph doesn't show any upward trend, and the pressure looks
like fluctuating about a central value.
Here is the .mdp file. Only changes made from the
previous .mdp for berendsen pressure coupling , are with pcoupl and tau_p.
; 7.3.3 Run Control
integrator = md
tinit = 0
dt = 0.002
nsteps = 2500000
comm_mode = Linear
nstcomm = 1
comm_grps = CHX SOL
; 7.3.8 Output Control
nstxout = 2500
nstvout = 2500
nstfout = 2500
nstlog = 2500
nstenergy = 100
nstxtcout = 1000
xtc_precision = 1000
xtc_grps = System
energygrps = System
; 7.3.9 Neighbor Searching
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 0.8
; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb = 0.8
; 7.3.11 VdW
vdwtype = cut-off
rvdw = 0.8
DispCorr = EnerPres
; 7.3.13 Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; 7.3.14 Temperature Coupling
tcoupl = nose-hoover
tc_grps = CHX SOL
tau_t = 0.5 0.5
ref_t = 298 298
; 7.3.15 Pressure Coupling
pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
; 7.3.17 Velocity Generation
gen_vel = no
; 7.3.18 Bonds
constraints = all-bonds
constraint_algorithm = LINCS
continuation = yes
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
"npt.mdp" 63L, 4080C
I guess there is something seriously wrong in the choice of
methods/parameters in the .mdp file, which I cant figure out. Kindly go
through and let me know your comments.
I would be happy to give any further details. Any help would be appreciated.
Regards,
Sujith
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