[gmx-users] Severe error with NPT

[sujithkakkat .]

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

107,4         Bot



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