[gmx-users] Dubious results with NPT

[sujithkakkat .]

Hello,

 After a while I got back to the problem posted here. This issue was the
large value for average  pressure(~25 bar against the reference pressure of
1 bar) in NPT simulations with parrinello rahman barostat. The system
studied is cyclohexane-water system with an interface.
The forcefield is Gromos96. Gromacs 4.6.5 version is used.

I recollect a post from Michael Shirts which says that with systems that
are heterogeneous in direction (not uniform in x y and z), any errors in
the pressure may be magnified. Is this what is  happening in my case?

Based on your suggestions , I tried the following to analyze/solve the
problem, and till now the results have not improved a bit.

 (i) The system was simplified. Each phases was simulated separately. The
results were good, with proper values of average pressure after NPT
simulation for both independent water and cyclohexane systems. However,
when doing the same with similar parameters on the water-cyclohexane
combined system with parrinello-rahman barostat , still gives very high
average pressure (even after 10ns )

 (ii) Changing the tau_p values did not help either. (I tried 1ps, 2ps,
and  4ps)

My question is whether, I can try the semiisotropic scaling? The manual
says that it is useful in case of systems with interface.  I am not sure,
since none of the replies I got suggested that option, which gives the
impression that it is not the best solution. But , to my limited knowledge
that is the only option left to be tried to solve the issue.


              The mdp file used is,

; 7.3.3 Run Control
integrator              = md
tinit                      = 0
dt                         = 0.001
nsteps                  = 10000000
comm_mode         = Linear
nstcomm              = 1
comm_grps           = CHX SOL

; 7.3.8 Output Control
nstxout                 = 25000
nstvout                 = 25000
nstfout                  = 25000
nstlog                   = 100
nstenergy              = 100
nstxtcout               = 100
xtc_precision          = 1000
xtc_grps                 = System
energygrps              = System

; 7.3.9 Neighbor Searching
nstlist                    = 10
ns_type                 = grid
pbc                       = xyz
rlist                       = 0.9

; 7.3.10 Electrostatics
coulombtype             = PME
rcoulomb                   = 0.9

; 7.3.11 VdW
vdwtype                 = cut-off
rvdw                      = 1.4
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                      = 2.0
compressibility        = 4.5e-5
ref_p                      = 1.0


; 7.3.17 Velocity Generation
gen_vel                   = no
gen_temp                = 298
gen_seed                 = -1

; 7.3.18 Bonds
constraints                 = none
constraint_algorithm    = LINCS
continuation                = no
lincs_order                  = 4
lincs_iter                     = 1
lincs_warnangle           = 30



Please comment.

Sujith.